How to filter out correlation table for P-value < 0.05 and coefficient > 0.06 and <-0.06 ?

[DC7]

Hi there!!! Here is a correlation table generated from my data frame with bacterial relative abundance. The 3rd and 4th columns respectively denotes correlation co-efficient (cor) and their P-value (p). Now, I want to filter this table to generate an output that will have interactions with p < 0.05 and cor > 0.6 and cor < -0.6.
Can anyone please tell me how can I do that? Here's a portion of table:

row	column	cor	p
Actinobaculum_sp_oral_taxon_183	Actinomyces_graevenitzii	-0.083166733306677	0.557766591033679
Actinobaculum_sp_oral_taxon_183	Actinomyces_naeslundii	-0.057666197516258	0.684693748325992
Actinomyces_graevenitzii	Actinomyces_naeslundii	-0.057666197516258	0.684693748325992
Actinobaculum_sp_oral_taxon_183	Actinomyces_odontolyticus	0.082972778302491	0.558688695520664
Actinomyces_graevenitzii	Actinomyces_odontolyticus	0.086259815138003	0.543159275510664
Actinomyces_naeslundii	Actinomyces_odontolyticus	0.260101357406385	0.062572519939439
Actinobaculum_sp_oral_taxon_183	Actinomyces_oris	0.001812984437111	0.989822610583224
Actinomyces_graevenitzii	Actinomyces_oris	0.078226921082765	0.581472276924872
Actinomyces_naeslundii	Actinomyces_oris	0.164725112347852	0.243223831404869
Actinomyces_odontolyticus	Actinomyces_oris	0.321304480536897	0.02020092245847
Actinobaculum_sp_oral_taxon_183	Actinomyces_sp_HMSC035G02	-0.009475829184974	0.946843170060088
Actinomyces_graevenitzii	Actinomyces_sp_HMSC035G02	0.223167925805104	0.111768183795273
Actinomyces_naeslundii	Actinomyces_sp_HMSC035G02	0.127195351524484	0.368876768685618
Actinomyces_odontolyticus	Actinomyces_sp_HMSC035G02	0.728031815255434	9.61068558069655E-10
Actinomyces_oris	Actinomyces_sp_HMSC035G02	0.489804314937454	0.000228307144797
Actinobaculum_sp_oral_taxon_183	Actinomyces_sp_HPA0247	-0.122407920609607	0.387315423215962

Many thanks
dc7

[FJCC]

If your data frame is named DF, you can get the result you want with the filter() function from dplyr.

library(dplyr)
DF_filtered <- filter(DF, abs(cor) > 0.6, p < 0.05)

[DC7]

I don't know why DF_fileterd doesn't contain a single negative (-ve) cor value. It is strange. Is it taking values only greater than 0.6? Also similar value coming multiple times:

Eisenbergiella_tayi	Ruthenibacterium_lactatiformans	0.679759843314795	2.99746081289243E-08
Clostridium_bolteae	Clostridium_symbiosum	0.68096900743543	2.77191414266298E-08
Eggerthella_lenta	Flavonifractor_plautii	0.685541202470124	2.05520234164425E-08
Actinomyces_naeslundii	Parascardovia_denticolens	0.68600532975442	1.99312686355313E-08
Bifidobacterium_pullorum	Rothia_dentocariosa	0.68600532975442	1.99312686355313E-08
Bifidobacterium_pullorum	Prevotella_sp_CAG_891	0.68600532975442	1.99312686355313E-08
Actinomyces_naeslundii	Parabacteroides_gordonii	0.68600532975442	1.99312686355313E-08
Prevotella_disiens	Bacillus_sp_FJAT_27916	0.68600532975442	1.99312686355313E-08
Bacteroides_sp_CAG_530	Enterococcus_hirae	0.68600532975442	1.99312686355313E-08
Bacteroides_sp_CAG_661	Enterococcus_hirae	0.68600532975442	1.99312686355313E-08
Prevotella_sp_AM42_24	Enterococcus_hirae	0.68600532975442	1.99312686355313E-08
Lactobacillus_acidophilus	Lactobacillus_amylovorus	0.68600532975442	1.99312686355313E-08
Prevotella_timonensis	Lactobacillus_crispatus	0.68600532975442	1.99312686355313E-08
Bacteroides_sp_CAG_530	Lactobacillus_fermentum	0.68600532975442	1.99312686355313E-08
Bacteroides_sp_CAG_661	Lactobacillus_fermentum	0.68600532975442	1.99312686355313E-08
Prevotella_sp_AM42_24	Lactobacillus_fermentum	0.68600532975442	1.99312686355313E-08
Bacteroides_sp_CAG_530	Lactobacillus_johnsonii	0.68600532975442	1.99312686355313E-08
Bacteroides_sp_CAG_661	Lactobacillus_johnsonii	0.68600532975442	1.99312686355313E-08
Prevotella_sp_AM42_24	Lactobacillus_johnsonii	0.68600532975442	1.99312686355313E-08

[FJCC]

Do you know that there are some rows where cor < -0.6? You can make a subset of the data to check that

NegCor <- filter(DF, cor < -0.6)

I also notice now that your p values can be greater than 1, so something is wrong with the construction of your data frame.

[DC7]

Yes. there was only one cor <-0.6 that I didn't notice earlier. However, where did you find P-value > 1? filter(final_mat, p > 1) This code shows no P-value greater than 1.

thanks
dc7

[FJCC]

I misread the data when I thought I saw p values above 1.