Hello everyone,
First, here is my source code..
Program=c("Trim_galore", "Cutadapt", "STAR", "VarScan2", "SomaticSniper", "MuTect2", "HT-seq")
Parameter=c('trim.quality=30\ntrim.clip_R1=13\ntrim.clip_R2=13','m=17 (Minimum read length)\nadapt.seq="TGGAATTCTCGGGTGCCAAGG"','sjdbOverhang=100 (ReadLength-1)\noutFilterMultimapScoreRange=1\noutFilterMultimapNmax=20\noutFilterMismatchNmax=10\nalignIntronMax=500000\nalignMatesGapMax=1000000\nsjdbScore=2\nalignSJDBoverhangMin=1\noutFilterMatchNminOverLread=0.33\noutFilterScoreMinOverLread=0.33','mapQ=1\nmin_coverage_normal=8\nmin_coverage_tumor=6\nmin_var_freq=0.10\nmin_freq_for_hom=0.75\nsomatic_p_value=0.05\nstrand_filter=0\nmin_tumor_freq=0.1\nmax_normal_freq=0.05\np_value=0.07','mapQual=1\nLOH=TRUE\nGenotype=TRUE\nsomaticQual=15\nsomaticMutation=0.01\nTheta=0.85\nHap.number=2\nHap.diff=0.001\nout.format="vcf"','minN=2\nsetKey="null"\nfilteredrecordsmergetype="KEEP_IF_ANY_UNFILTERED"\ncontamination_fraction_to_filter=0.02','Mode="intersection-nonempty"\nstranded="no"\nidattr="gene_id"\nhtseq.r="pos"\nhtseq.a=10')
program.df=data.frame(Program=Program,Parameter=Parameter, row.names = NULL)
program.df$Program=as.character(program.df$Program)
pander(program.df, justify = "center", style = "grid", keep.line.breaks = TRUE, split.cells = c("50%","50%"), emphasize.strong.cols = 1)
The others come out well, but only "STAR" comes out strange.
If you know what the problem is, please help me.
