Error in contrasts<-(*tmp*, value = contr.funs[1 + isOF[nn]]) : contrasts can be applied only to factors with 2 or more levels

Hi,

I have encountered an error while running the stattest function of ballgown

I have run the command as

 results_transcripts = stattest(bg_chrX_filt,feature= c("gene","exon","intron","transcript"),covariate="part", getFC=TRUE,meas="FPKM", timecourse = FALSE, df=2)

The error was
Error in contrasts<-(tmp, value = contr.funs[1 + isOF[nn]]) :
contrasts can be applied only to factors with 2 or more levels

Again I modified the above command. The command is

results_transcripts = stattest(bg_chrX_filt,feature= c("gene","exon","intron","transcript"),covariate="part", getFC=TRUE,meas="FPKM", timecourse = TRUE)

The error was

Error in contrasts<-(*tmp*, value = contr.funs[1 + isOF[nn]]) :
contrasts can be applied only to factors with 2 or more levels
In addition: Warning message:
In stattest(bg_chrX_filt, feature = c("gene", "exon", "intron", :
Not enough timepoints (or values of covariate) to fit a spline model with 4 degrees of freedom. Statistical tests will be run treating time as categorical. You can also re-run the analysis with decreased df.

It's hard to pinpoint without a reproducible example, called a reprex, but a function expects a factor argument with two or more level and isn't seeing it.

Take a look at your environment

ls()

for objects that you know or suspect the function may be operating on, then

str(obj)

inspect the structure of the object. If there are factors, it will tell you how many levels.

Hi technocrat,
I just do

ls()
[1] "bg_chrX" "bg_chrX_filt" "data_directory" "pheno_data" "stattest"

str(stattest)

function (gown = NULL, gowntable = NULL, pData = NULL, mod = NULL, mod0 = NULL, feature = c("gene",
"exon", "intron", "transcript"), meas = c("cov", "FPKM", "rcount", "ucount", "mrcount",
"mcov"), timecourse = FALSE, covariate = NULL, adjustvars = NULL, gexpr = NULL, df = 4,
getFC = FALSE, libadjust = NULL, log = TRUE)

  • attr(, "srcref")=Class 'srcref' atomic [1:8] 1 12 210 1 12 1 1 210
    .. ..- attr(
    , "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x487b4058>

I did not now how to resolve this error .I just send you result of two commands that you gave me .how tell next what to do resolve this issue

str(bg_chrX)
Formal class 'ballgown' [package "ballgown"] with 7 slots
..@ expr :List of 3
.. .. intron:'data.frame': 477939 obs. of 23 variables: .. .. .. i_id : int [1:477939] 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. chr : chr [1:477939] "1A" "1A" "1A" "1A" ... .. .. .. strand : chr [1:477939] "+" "+" "+" "+" ...
.. .. .. start : int [1:477939] 565 565 565 946 10217 565 25024 1447 6240 6458 ... .. .. .. end : int [1:477939] 9703 12708 15713 10084 25201 24688 42035 10585 46979 56213 ...
.. .. .. rcount.G1 : int [1:477939] 21 4 8 28 0 0 5 0 162 157 ... .. .. .. ucount.G1 : int [1:477939] 8 0 0 2 0 0 3 0 88 29 ...
.. .. .. mrcount.G1: num [1:477939] 12.02 1.2 2.62 11.3 0 ... .. .. .. rcount.G2 : int [1:477939] 204 72 83 32 45 3 8 1 20 32 ...
.. .. .. ucount.G2 : int [1:477939] 28 0 0 5 41 0 3 0 5 3 ... .. .. .. mrcount.G2: num [1:477939] 74.4 18.7 22.5 15.3 43 ...
.. .. .. rcount.G3 : int [1:477939] 6 4 5 25 0 0 3 122 0 10 ... .. .. .. ucount.G3 : int [1:477939] 0 0 0 1 0 0 2 75 0 0 ...
.. .. .. mrcount.G3: num [1:477939] 2 1.25 1.75 9.17 0 ... .. .. .. rcount.G4 : int [1:477939] 6 2 6 9 0 0 2 0 16 20 ...
.. .. .. ucount.G4 : int [1:477939] 1 0 1 6 0 0 1 0 9 3 ... .. .. .. mrcount.G4: num [1:477939] 2.73 0.53 2.73 7.5 0 0 1.5 0 11.7 9.83 ...
.. .. .. rcount.G5 : int [1:477939] 3 1 3 5 0 0 0 0 13 3 ... .. .. .. ucount.G5 : int [1:477939] 0 0 0 1 0 0 0 0 8 0 ...
.. .. .. mrcount.G5: num [1:477939] 1.33 0.33 1.33 3 0 ... .. .. .. rcount.G6 : int [1:477939] 0 0 0 8 0 0 1 0 5 0 ...
.. .. .. ucount.G6 : int [1:477939] 0 0 0 2 0 0 1 0 3 0 ... .. .. .. mrcount.G6: num [1:477939] 0 0 0 5 0 0 1 0 3.58 0 ...
.. .. exon :'data.frame': 662545 obs. of 47 variables: .. .. .. e_id : int [1:662545] 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. chr : chr [1:662545] "1A" "1A" "1A" "1A" ... .. .. .. strand : chr [1:662545] "+" "+" "+" "+" ...
.. .. .. start : int [1:662545] 200 200 9704 371 12709 15714 371 10085 25202 24689 ... .. .. .. end : int [1:662545] 1683 564 9894 564 13827 16832 945 10216 25625 25023 ...
.. .. .. rcount.G1 : int [1:662545] 503 58 83 53 71 145 170 41 239 46 ... .. .. .. ucount.G1 : int [1:662545] 106 25 9 22 6 15 46 2 141 19 ...
.. .. .. mrcount.G1: num [1:662545] 241.2 35 29.2 31.5 24.9 ... .. .. .. cov.G1 : num [1:662545] 37.24 14.98 57.55 27.04 8.68 ...
.. .. .. cov_sd.G1 : num [1:662545] 38.9 17.5 37.3 16.2 12 ... .. .. .. mcov.G1 : num [1:662545] 16.4 10.13 18.57 18.58 2.31 ...
.. .. .. mcov_sd.G1: num [1:662545] 16.08 11.16 12.26 9 3.09 ... .. .. .. rcount.G2 : int [1:662545] 1124 418 625 412 250 457 572 99 405 117 ...
.. .. .. ucount.G2 : int [1:662545] 152 57 42 54 13 57 93 42 244 18 ... .. .. .. mrcount.G2: num [1:662545] 448.4 155.7 206.8 151.9 77.7 ...
.. .. .. cov.G2 : num [1:662545] 80.8 107 371 199.8 41.6 ... .. .. .. cov_sd.G2 : num [1:662545] 95.9 153.3 267.8 160.7 87.9 ...
.. .. .. mcov.G2 : num [1:662545] 31.4 40.8 121.4 76 11.7 ... .. .. .. mcov_sd.G2: num [1:662545] 35 53.2 84.8 51.8 23.6 ...
.. .. .. rcount.G3 : int [1:662545] 996 34 14 34 84 131 114 35 175 18 ... .. .. .. ucount.G3 : int [1:662545] 71 8 0 8 6 21 31 1 109 8 ...
.. .. .. mrcount.G3: num [1:662545] 318.28 18 4.23 18 25.5 ... .. .. .. cov.G3 : num [1:662545] 83.84 10.06 8.16 18.92 7.27 ...
.. .. .. cov_sd.G3 : num [1:662545] 156.29 14.45 3.09 15.01 11.03 ... .. .. .. mcov.G3 : num [1:662545] 25.6 6.29 1.84 11.84 1.77 ...
.. .. .. mcov_sd.G3: num [1:662545] 37.04 8.85 1.12 8.93 3.13 ... .. .. .. rcount.G4 : int [1:662545] 272 28 9 24 33 67 61 15 97 19 ...
.. .. .. ucount.G4 : int [1:662545] 52 12 1 9 4 15 30 7 60 11 ... .. .. .. mrcount.G4: num [1:662545] 121.37 17.33 3.47 14 11.22 ...
.. .. .. cov.G4 : num [1:662545] 21.44 9.27 4.18 16.73 3.7 ... .. .. .. cov_sd.G4 : num [1:662545] 22.22 10.33 4.06 9 4.6 ...
.. .. .. mcov.G4 : num [1:662545] 8.754 6.219 1.052 11.149 0.867 ... .. .. .. mcov_sd.G4: num [1:662545] 8.81 6.28 1.46 4.44 1.2 ...
.. .. .. rcount.G5 : int [1:662545] 199 14 10 13 27 47 36 12 112 12 ... .. .. .. ucount.G5 : int [1:662545] 49 7 0 6 1 20 17 5 72 4 ...
.. .. .. mrcount.G5: num [1:662545] 101.45 10 3.42 9 9.27 ... .. .. .. cov.G5 : num [1:662545] 15.7 4.5 5.12 8.42 3.14 ...
.. .. .. cov_sd.G5 : num [1:662545] 21.05 5.76 1.19 5.43 2.48 ... .. .. .. mcov.G5 : num [1:662545] 7.4 3.59 1.34 6.72 0.72 ...
.. .. .. mcov_sd.G5: num [1:662545] 9.185 4.375 0.557 3.877 0.776 ... .. .. .. rcount.G6 : int [1:662545] 155 4 4 4 23 33 36 15 66 4 ...
.. .. .. ucount.G6 : int [1:662545] 25 3 0 3 0 6 13 2 47 2 ... .. .. .. mrcount.G6: num [1:662545] 61.98 3.25 1.42 3.25 5.43 ...
.. .. .. cov.G6 : num [1:662545] 12.23 2.31 3.69 4.35 2.3 ... .. .. .. cov_sd.G6 : num [1:662545] 15.47 2.77 2.94 2.35 2.59 ...
.. .. .. mcov.G6 : num [1:662545] 4.21 2.077 0.843 3.907 0.247 ... .. .. .. mcov_sd.G6: num [1:662545] 4.438 2.479 0.962 1.98 0.707 ...
.. .. trans :'data.frame': 195181 obs. of 22 variables: .. .. .. t_id : int [1:195181] 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. chr : chr [1:195181] "1A" "1A" "1A" "1A" ... .. .. .. strand : Factor w/ 3 levels "-",".","+": 3 3 3 3 3 3 1 3 3 3 ...
.. .. .. start : int [1:195181] 200 200 371 371 371 371 1372 5014 5014 5014 ... .. .. .. end : int [1:195181] 1683 9894 13827 16832 25625 42817 10821 47573 56356 56588 ...
.... .. t_name : chr [1:195181] "ENSRNA050013875-T1" "MSTRG.165.1" "MSTRG.165.6" "MSTRG.165.5" ... .. .. .. num_exons: int [1:195181] 1 2 2 2 3 3 2 2 2 3 ...
.. .. .. length : int [1:195181] 1484 556 1313 1313 1131 1311 311 1820 1587 1818 ... .. .. .. gene_id : chr [1:195181] "MSTRG.165" "MSTRG.165" "MSTRG.165" "MSTRG.165" ...
.. .. .. gene_name: chr [1:195181] "LSU_rRNA_eukarya" "." "." "." ... .. .. .. cov.G1 : num [1:195181] 10.159 7.899 0.524 1.26 1.908 ...
.. .. .. FPKM.G1 : num [1:195181] 0.9166 0.7127 0.0472 0.1136 0.1721 ... .. .. .. cov.G2 : num [1:195181] 14.71 50.52 3.95 5.1 32.91 ...
.. .. .. FPKM.G2 : num [1:195181] 1.365 4.687 0.366 0.473 3.053 ... .. .. .. cov.G3 : num [1:195181] 22.05 1.16 1.72 1.47 1.34 ...
.. .. .. FPKM.G3 : num [1:195181] 2.015 0.106 0.157 0.134 0.123 ... .. .. .. cov.G4 : num [1:195181] 5.97 1.263 0.909 1.837 1.456 ...
.. .. .. FPKM.G4 : num [1:195181] 0.4918 0.104 0.0749 0.1514 0.12 ... .. .. .. cov.G5 : num [1:195181] 5.347 0.849 0.799 1.298 0.89 ...
.. .. .. FPKM.G5 : num [1:195181] 0.4561 0.0724 0.0682 0.1107 0.076 ... .. .. .. cov.G6 : num [1:195181] 3.283 0.321 0 0 5.87 ...
.. .. .. FPKM.G6 : num [1:195181] 0.2818 0.0275 0 0 0.5038 ... ..@ indexes :List of 5 .. .. e2t :'data.frame': 1016843 obs. of 2 variables:
.. .. .. e_id: int [1:1016843] 1 2 3 4 5 4 6 7 8 9 ... .. .. .. t_id: int [1:1016843] 1 2 2 3 3 4 4 5 5 5 ...
.. .. i2t :'data.frame': 821662 obs. of 2 variables: .. .. .. i_id: int [1:821662] 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. t_id: int [1:821662] 2 3 4 5 5 6 6 7 8 9 ... .. .. t2g :'data.frame': 195181 obs. of 2 variables:
.. .. .. t_id: int [1:195181] 1 2 3 4 5 6 7 8 9 10 ... .. .. .. g_id: Factor w/ 140219 levels "ENSRNA050007810",..: 18139 18139 18139 18139 18139 18139 18250 18361 18361 18361 ...
.. .. bamfiles: NULL .. .. pData :'data.frame': 6 obs. of 2 variables:
.. .. .. Ids : Factor w/ 6 levels "G1","G2","G3",..: 1 2 3 4 5 6 .. .. .. part: Factor w/ 1 level "root": 1 1 1 1 1 1
..@ structure :List of 3
.. .. intron:Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 22 levels "1A","1B","1D",..: 1 2 3 4 5 6 7 8 9 10 ... .. .. .. .. .. ..@ lengths : int [1:22] 20103 21478 20017 25559 26966 25718 23873 25928 23993 21607 ... .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. ..@ start : int [1:477939] 565 565 565 946 10217 565 25024 1447 6240 6458 ... .. .. .. .. .. ..@ width : int [1:477939] 9139 12144 15149 9139 14985 24124 17012 9139 40740 49756 ... .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 1 2 1 2 1 2 1 2 ... .. .. .. .. .. ..@ lengths : int [1:44546] 7 1 7 2 9 1 11 2 11 4 ... .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 477939 .. .. .. .. .. ..@ listData :List of 2 .. .. .. .. .. .. .. id : int [1:477939] 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. .. .. .. .. transcripts: chr [1:477939] "2" "3" "4" "5" ... .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr [1:22] "1A" "1B" "1D" "2A" ... .. .. .. .. .. ..@ seqlengths : int [1:22] NA NA NA NA NA NA NA NA NA NA ... .. .. .. .. .. ..@ is_circular: logi [1:22] NA NA NA NA NA NA ... .. .. .. .. .. ..@ genome : chr [1:22] NA NA NA NA ... .. .. .. ..@ metadata : list() .. .. exon :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots
.. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots
.. .. .. .. .. ..@ values : Factor w/ 22 levels "1A","1B","1D",..: 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. .. .. ..@ lengths : int [1:22] 27560 30172 27461 34945 37086 34949 32459 35653 32446 29586 ...
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots
.. .. .. .. .. ..@ start : int [1:662545] 200 200 9704 371 12709 15714 371 10085 25202 24689 ...
.. .. .. .. .. ..@ width : int [1:662545] 1484 365 191 194 1119 1119 575 132 424 335 ...
.. .. .. .. .. ..@ NAMES : NULL
.. .. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots
.. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","": 1 2 1 2 1 2 1 2 1 2 ...
.. .. .. .. .. ..@ lengths : int [1:68269] 11 2 13 3 17 2 17 4 16 6 ...
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. .. .. ..@ rownames : NULL
.. .. .. .. .. ..@ nrows : int 662545
.. .. .. .. .. ..@ listData :List of 2
.. .. .. .. .. .. .. id : int [1:662545] 1 2 3 4 5 6 7 8 9 10 ... .. .. .. .. .. .. .. transcripts: chr [1:662545] "1" "2" "2" "c(3, 4, 6)" ...
.. .. .. .. .. ..@ elementType : chr "ANY"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots
.. .. .. .. .. ..@ seqnames : chr [1:22] "1A" "1B" "1D" "2A" ...
.. .. .. .. .. ..@ seqlengths : int [1:22] NA NA NA NA NA NA NA NA NA NA ...
.. .. .. .. .. ..@ is_circular: logi [1:22] NA NA NA NA NA NA ...
.. .. .. .. .. ..@ genome : chr [1:22] NA NA NA NA ...
.. .. .. ..@ metadata : list()
.. .. trans :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 22 levels "1A","1B","1D",..: 1 2 3 4 5 6 7 8 9 10 ... .. .. .. .. .. .. .. ..@ lengths : int [1:22] 41983 45806 42358 54084 55831 53715 52863 55985 53674 45475 ... .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:1016843] 200 200 9704 371 12709 371 15714 371 10085 25202 ... .. .. .. .. .. .. .. ..@ width : int [1:1016843] 1484 365 191 194 1119 194 1119 575 132 424 ... .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 1 2 1 2 1 2 1 2 ... .. .. .. .. .. .. .. ..@ lengths : int [1:68273] 13 2 13 3 18 2 17 4 19 6 ... .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 1016843 .. .. .. .. .. .. .. ..@ listData :List of 2 .. .. .. .. .. .. .. .. .. id : int [1:1016843] 1 2 3 4 5 4 6 7 8 9 ...
.. .. .. .. .. .. .. .. ..$ transcripts: chr [1:1016843] "1" "2" "2" "c(3, 4, 6)" ...
.. .. .. .. .. .. .. ..@ elementType : chr "ANY"
.. .. .. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. .. .. ..@ metadata : list()
.. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots
.. .. .. .. .. .. .. ..@ seqnames : chr [1:22] "1A" "1B" "1D" "2A" ...
.. .. .. .. .. .. .. ..@ seqlengths : int [1:22] NA NA NA NA NA NA NA NA NA NA ...
.. .. .. .. .. .. .. ..@ is_circular: logi [1:22] NA NA NA NA NA NA ...
.. .. .. .. .. .. .. ..@ genome : chr [1:22] NA NA NA NA ...
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. .. .. ..@ rownames : NULL
.. .. .. .. .. ..@ nrows : int 195181
.. .. .. .. .. ..@ listData : Named list()
.. .. .. .. .. ..@ elementType : chr "ANY"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots
.. .. .. .. .. ..@ end : int [1:195181] 1 3 5 7 10 13 15 17 19 22 ...
.. .. .. .. .. ..@ NAMES : chr [1:195181] "1" "2" "3" "4" ...
.. .. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ elementType : chr "GRanges"
.. .. .. ..@ metadata : list()
..@ dirs : Named chr [1:6] "/home/shahana/R/x86_64-pc-linux-gnu-library/3.4/ballgown/extdata/G1" "/home/shahana/R/x86_64-pc-linux-gnu-library/3.4/ballgown/extdata/G2" "/home/shahana/R/x86_64-pc-linux-gnu-library/3.4/ballgown/extdata/G3" "/home/shahana/R/x86_64-pc-linux-gnu-library/3.4/ballgown/extdata/G4" ...
.. ..- attr(
, "names")= chr [1:6] "G1" "G2" "G3" "G4" ...
..@ mergedDate: chr "Sat Apr 13 16:08:19 2019"
..@ meas : chr "all"
..@ RSEM : logi FALSE

str(bg_chrX_filt)
Formal class 'ballgown' [package "ballgown"] with 7 slots
..@ expr :List of 3
.. .. intron:'data.frame': 477939 obs. of 23 variables: .. .. .. i_id : int [1:477939] 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. chr : chr [1:477939] "1A" "1A" "1A" "1A" ... .. .. .. strand : chr [1:477939] "+" "+" "+" "+" ...
.. .. .. start : int [1:477939] 565 565 565 946 10217 565 25024 1447 6240 6458 ... .. .. .. end : int [1:477939] 9703 12708 15713 10084 25201 24688 42035 10585 46979 56213 ...
.. .. .. rcount.G1 : int [1:477939] 21 4 8 28 0 0 5 0 162 157 ... .. .. .. ucount.G1 : int [1:477939] 8 0 0 2 0 0 3 0 88 29 ...
.. .. .. mrcount.G1: num [1:477939] 12.02 1.2 2.62 11.3 0 ... .. .. .. rcount.G2 : int [1:477939] 204 72 83 32 45 3 8 1 20 32 ...
.. .. .. ucount.G2 : int [1:477939] 28 0 0 5 41 0 3 0 5 3 ... .. .. .. mrcount.G2: num [1:477939] 74.4 18.7 22.5 15.3 43 ...
.. .. .. rcount.G3 : int [1:477939] 6 4 5 25 0 0 3 122 0 10 ... .. .. .. ucount.G3 : int [1:477939] 0 0 0 1 0 0 2 75 0 0 ...
.. .. .. mrcount.G3: num [1:477939] 2 1.25 1.75 9.17 0 ... .. .. .. rcount.G4 : int [1:477939] 6 2 6 9 0 0 2 0 16 20 ...
.. .. .. ucount.G4 : int [1:477939] 1 0 1 6 0 0 1 0 9 3 ... .. .. .. mrcount.G4: num [1:477939] 2.73 0.53 2.73 7.5 0 0 1.5 0 11.7 9.83 ...
.. .. .. rcount.G5 : int [1:477939] 3 1 3 5 0 0 0 0 13 3 ... .. .. .. ucount.G5 : int [1:477939] 0 0 0 1 0 0 0 0 8 0 ...
.. .. .. mrcount.G5: num [1:477939] 1.33 0.33 1.33 3 0 ... .. .. .. rcount.G6 : int [1:477939] 0 0 0 8 0 0 1 0 5 0 ...
.. .. .. ucount.G6 : int [1:477939] 0 0 0 2 0 0 1 0 3 0 ... .. .. .. mrcount.G6: num [1:477939] 0 0 0 5 0 0 1 0 3.58 0 ...
.. .. exon :'data.frame': 662545 obs. of 47 variables: .. .. .. e_id : int [1:662545] 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. chr : chr [1:662545] "1A" "1A" "1A" "1A" ... .. .. .. strand : chr [1:662545] "+" "+" "+" "+" ...
.. .. .. start : int [1:662545] 200 200 9704 371 12709 15714 371 10085 25202 24689 ... .. .. .. end : int [1:662545] 1683 564 9894 564 13827 16832 945 10216 25625 25023 ...
.. .. .. rcount.G1 : int [1:662545] 503 58 83 53 71 145 170 41 239 46 ... .. .. .. ucount.G1 : int [1:662545] 106 25 9 22 6 15 46 2 141 19 ...
.. .. .. mrcount.G1: num [1:662545] 241.2 35 29.2 31.5 24.9 ... .. .. .. cov.G1 : num [1:662545] 37.24 14.98 57.55 27.04 8.68 ...
.. .. .. cov_sd.G1 : num [1:662545] 38.9 17.5 37.3 16.2 12 ... .. .. .. mcov.G1 : num [1:662545] 16.4 10.13 18.57 18.58 2.31 ...
.. .. .. mcov_sd.G1: num [1:662545] 16.08 11.16 12.26 9 3.09 ... .. .. .. rcount.G2 : int [1:662545] 1124 418 625 412 250 457 572 99 405 117 ...
.. .. .. ucount.G2 : int [1:662545] 152 57 42 54 13 57 93 42 244 18 ... .. .. .. mrcount.G2: num [1:662545] 448.4 155.7 206.8 151.9 77.7 ...
.. .. .. cov.G2 : num [1:662545] 80.8 107 371 199.8 41.6 ... .. .. .. cov_sd.G2 : num [1:662545] 95.9 153.3 267.8 160.7 87.9 ...
.. .. .. mcov.G2 : num [1:662545] 31.4 40.8 121.4 76 11.7 ... .. .. .. mcov_sd.G2: num [1:662545] 35 53.2 84.8 51.8 23.6 ...
.. .. .. rcount.G3 : int [1:662545] 996 34 14 34 84 131 114 35 175 18 ... .. .. .. ucount.G3 : int [1:662545] 71 8 0 8 6 21 31 1 109 8 ...
.. .. .. mrcount.G3: num [1:662545] 318.28 18 4.23 18 25.5 ... .. .. .. cov.G3 : num [1:662545] 83.84 10.06 8.16 18.92 7.27 ...
.. .. .. cov_sd.G3 : num [1:662545] 156.29 14.45 3.09 15.01 11.03 ... .. .. .. mcov.G3 : num [1:662545] 25.6 6.29 1.84 11.84 1.77 ...
.. .. .. mcov_sd.G3: num [1:662545] 37.04 8.85 1.12 8.93 3.13 ... .. .. .. rcount.G4 : int [1:662545] 272 28 9 24 33 67 61 15 97 19 ...
.. .. .. ucount.G4 : int [1:662545] 52 12 1 9 4 15 30 7 60 11 ... .. .. .. mrcount.G4: num [1:662545] 121.37 17.33 3.47 14 11.22 ...
.. .. .. cov.G4 : num [1:662545] 21.44 9.27 4.18 16.73 3.7 ... .. .. .. cov_sd.G4 : num [1:662545] 22.22 10.33 4.06 9 4.6 ...
.. .. .. mcov.G4 : num [1:662545] 8.754 6.219 1.052 11.149 0.867 ... .. .. .. mcov_sd.G4: num [1:662545] 8.81 6.28 1.46 4.44 1.2 ...
.. .. .. rcount.G5 : int [1:662545] 199 14 10 13 27 47 36 12 112 12 ... .. .. .. ucount.G5 : int [1:662545] 49 7 0 6 1 20 17 5 72 4 ...
.. .. .. mrcount.G5: num [1:662545] 101.45 10 3.42 9 9.27 ... .. .. .. cov.G5 : num [1:662545] 15.7 4.5 5.12 8.42 3.14 ...
.. .. .. cov_sd.G5 : num [1:662545] 21.05 5.76 1.19 5.43 2.48 ... .. .. .. mcov.G5 : num [1:662545] 7.4 3.59 1.34 6.72 0.72 ...
.. .. .. mcov_sd.G5: num [1:662545] 9.185 4.375 0.557 3.877 0.776 ... .. .. .. rcount.G6 : int [1:662545] 155 4 4 4 23 33 36 15 66 4 ...
.. .. .. ucount.G6 : int [1:662545] 25 3 0 3 0 6 13 2 47 2 ... .. .. .. mrcount.G6: num [1:662545] 61.98 3.25 1.42 3.25 5.43 ...
.. .. .. cov.G6 : num [1:662545] 12.23 2.31 3.69 4.35 2.3 ... .. .. .. cov_sd.G6 : num [1:662545] 15.47 2.77 2.94 2.35 2.59 ...
.. .. .. mcov.G6 : num [1:662545] 4.21 2.077 0.843 3.907 0.247 ... .. .. .. mcov_sd.G6: num [1:662545] 4.438 2.479 0.962 1.98 0.707 ...
.. .. trans :'data.frame': 195181 obs. of 22 variables: .. .. .. t_id : int [1:195181] 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. chr : chr [1:195181] "1A" "1A" "1A" "1A" ... .. .. .. strand : Factor w/ 3 levels "-",".","+": 3 3 3 3 3 3 1 3 3 3 ...
.. .. .. start : int [1:195181] 200 200 371 371 371 371 1372 5014 5014 5014 ... .. .. .. end : int [1:195181] 1683 9894 13827 16832 25625 42817 10821 47573 56356 56588 ...
.. .. .. t_name : chr [1:195181] "ENSRNA050013875-T1" "MSTRG.165.1" "MSTRG.165.6" "MSTRG.165.5" ... .. .. .. num_exons: int [1:195181] 1 2 2 2 3 3 2 2 2 3 ...
.. .. .. length : int [1:195181] 1484 556 1313 1313 1131 1311 311 1820 1587 1818 ... .. .. .. gene_id : chr [1:195181] "MSTRG.165" "MSTRG.165" "MSTRG.165" "MSTRG.165" ...
.. .. .. gene_name: chr [1:195181] "LSU_rRNA_eukarya" "." "." "." ... .. .. .. cov.G1 : num [1:195181] 10.159 7.899 0.524 1.26 1.908 ...
.. .. .. FPKM.G1 : num [1:195181] 0.9166 0.7127 0.0472 0.1136 0.1721 ... .. .. .. cov.G2 : num [1:195181] 14.71 50.52 3.95 5.1 32.91 ...
.. .. .. FPKM.G2 : num [1:195181] 1.365 4.687 0.366 0.473 3.053 ... .. .. .. cov.G3 : num [1:195181] 22.05 1.16 1.72 1.47 1.34 ...
.. .. .. FPKM.G3 : num [1:195181] 2.015 0.106 0.157 0.134 0.123 ... .. .. .. cov.G4 : num [1:195181] 5.97 1.263 0.909 1.837 1.456 ...
.. .. .. FPKM.G4 : num [1:195181] 0.4918 0.104 0.0749 0.1514 0.12 ... .. .. .. cov.G5 : num [1:195181] 5.347 0.849 0.799 1.298 0.89 ...
.. .. .. FPKM.G5 : num [1:195181] 0.4561 0.0724 0.0682 0.1107 0.076 ... .. .. .. cov.G6 : num [1:195181] 3.283 0.321 0 0 5.87 ...
.. .. .. FPKM.G6 : num [1:195181] 0.2818 0.0275 0 0 0.5038 ... ..@ indexes :List of 5 .. .. e2t :'data.frame': 1016843 obs. of 2 variables:
.. .. .. e_id: int [1:1016843] 1 2 3 4 5 4 6 7 8 9 ... .. .. .. t_id: int [1:1016843] 1 2 2 3 3 4 4 5 5 5 ...
.. .. i2t :'data.frame': 821662 obs. of 2 variables: .. .. .. i_id: int [1:821662] 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. t_id: int [1:821662] 2 3 4 5 5 6 6 7 8 9 ... .. .. t2g :'data.frame': 195181 obs. of 2 variables:
.. .. .. t_id: int [1:195181] 1 2 3 4 5 6 7 8 9 10 ... .. .. .. g_id: Factor w/ 140219 levels "ENSRNA050007810",..: 18139 18139 18139 18139 18139 18139 18250 18361 18361 18361 ...
.. .. bamfiles: NULL .. .. pData :'data.frame': 6 obs. of 2 variables:
.. .. .. Ids : Factor w/ 6 levels "G1","G2","G3",..: 1 2 3 4 5 6 .. .. .. part: Factor w/ 1 level "root": 1 1 1 1 1 1
..@ structure :List of 3
.. .. intron:Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 22 levels "1A","1B","1D",..: 1 2 3 4 5 6 7 8 9 10 ... .. .. .. .. .. ..@ lengths : int [1:22] 20103 21478 20017 25559 26966 25718 23873 25928 23993 21607 ... .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. ..@ start : int [1:477939] 565 565 565 946 10217 565 25024 1447 6240 6458 ... .. .. .. .. .. ..@ width : int [1:477939] 9139 12144 15149 9139 14985 24124 17012 9139 40740 49756 ... .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 1 2 1 2 1 2 1 2 ... .. .. .. .. .. ..@ lengths : int [1:44546] 7 1 7 2 9 1 11 2 11 4 ... .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. ..@ nrows : int 477939 .. .. .. .. .. ..@ listData :List of 2 .. .. .. .. .. .. .. id : int [1:477939] 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. .. .. .. .. transcripts: chr [1:477939] "2" "3" "4" "5" ... .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. ..@ seqnames : chr [1:22] "1A" "1B" "1D" "2A" ... .. .. .. .. .. ..@ seqlengths : int [1:22] NA NA NA NA NA NA NA NA NA NA ... .. .. .. .. .. ..@ is_circular: logi [1:22] NA NA NA NA NA NA ... .. .. .. .. .. ..@ genome : chr [1:22] NA NA NA NA ... .. .. .. ..@ metadata : list() .. .. exon :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots
.. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots
.. .. .. .. .. ..@ values : Factor w/ 22 levels "1A","1B","1D",..: 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. .. .. ..@ lengths : int [1:22] 27560 30172 27461 34945 37086 34949 32459 35653 32446 29586 ...
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots
.. .. .. .. .. ..@ start : int [1:662545] 200 200 9704 371 12709 15714 371 10085 25202 24689 ...
.. .. .. .. .. ..@ width : int [1:662545] 1484 365 191 194 1119 1119 575 132 424 335 ...
.. .. .. .. .. ..@ NAMES : NULL
.. .. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots
.. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","": 1 2 1 2 1 2 1 2 1 2 ...
.. .. .. .. .. ..@ lengths : int [1:68269] 11 2 13 3 17 2 17 4 16 6 ...
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. .. .. ..@ rownames : NULL
.. .. .. .. .. ..@ nrows : int 662545
.. .. .. .. .. ..@ listData :List of 2
.. .. .. .. .. .. .. id : int [1:662545] 1 2 3 4 5 6 7 8 9 10 ... .. .. .. .. .. .. .. transcripts: chr [1:662545] "1" "2" "2" "c(3, 4, 6)" ...
.. .. .. .. .. ..@ elementType : chr "ANY"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots
.. .. .. .. .. ..@ seqnames : chr [1:22] "1A" "1B" "1D" "2A" ...
.. .. .. .. .. ..@ seqlengths : int [1:22] NA NA NA NA NA NA NA NA NA NA ...
.. .. .. .. .. ..@ is_circular: logi [1:22] NA NA NA NA NA NA ...
.. .. .. .. .. ..@ genome : chr [1:22] NA NA NA NA ...
.. .. .. ..@ metadata : list()
.. .. trans :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 22 levels "1A","1B","1D",..: 1 2 3 4 5 6 7 8 9 10 ... .. .. .. .. .. .. .. ..@ lengths : int [1:22] 41983 45806 42358 54084 55831 53715 52863 55985 53674 45475 ... .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:1016843] 200 200 9704 371 12709 371 15714 371 10085 25202 ... .. .. .. .. .. .. .. ..@ width : int [1:1016843] 1484 365 191 194 1119 194 1119 575 132 424 ... .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 1 2 1 2 1 2 1 2 1 2 ... .. .. .. .. .. .. .. ..@ lengths : int [1:68273] 13 2 13 3 18 2 17 4 19 6 ... .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 1016843 .. .. .. .. .. .. .. ..@ listData :List of 2 .. .. .. .. .. .. .. .. .. id : int [1:1016843] 1 2 3 4 5 4 6 7 8 9 ...
.. .. .. .. .. .. .. .. ..$ transcripts: chr [1:1016843] "1" "2" "2" "c(3, 4, 6)" ...
.. .. .. .. .. .. .. ..@ elementType : chr "ANY"
.. .. .. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. .. .. ..@ metadata : list()
.. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots
.. .. .. .. .. .. .. ..@ seqnames : chr [1:22] "1A" "1B" "1D" "2A" ...
.. .. .. .. .. .. .. ..@ seqlengths : int [1:22] NA NA NA NA NA NA NA NA NA NA ...
.. .. .. .. .. .. .. ..@ is_circular: logi [1:22] NA NA NA NA NA NA ...
.. .. .. .. .. .. .. ..@ genome : chr [1:22] NA NA NA NA ...
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. .. .. ..@ rownames : NULL
.. .. .. .. .. ..@ nrows : int 195181
.. .. .. .. .. ..@ listData : Named list()
.. .. .. .. .. ..@ elementType : chr "ANY"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots
.. .. .. .. .. ..@ end : int [1:195181] 1 3 5 7 10 13 15 17 19 22 ...
.. .. .. .. .. ..@ NAMES : chr [1:195181] "1" "2" "3" "4" ...
.. .. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ elementType : chr "GRanges"
.. .. .. ..@ metadata : list()
..@ dirs : Named chr [1:6] "/home/shahana/R/x86_64-pc-linux-gnu-library/3.4/ballgown/extdata/G1" "/home/shahana/R/x86_64-pc-linux-gnu-library/3.4/ballgown/extdata/G2" "/home/shahana/R/x86_64-pc-linux-gnu-library/3.4/ballgown/extdata/G3" "/home/shahana/R/x86_64-pc-linux-gnu-library/3.4/ballgown/extdata/G4" ...
.. ..- attr(
, "names")= chr [1:6] "G1" "G2" "G3" "G4" ...
..@ mergedDate: chr "Sat Apr 13 16:08:19 2019"
..@ meas : chr "all"
..@ RSEM : logi FALSE

ENSRNA050007810 is suspect. A data frame column with the heading Factorw doesn't make its contents a factor. For that you should 1) rename the column and two apply as.factor(new_name_of_column

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