Question: Saving output from glmTreat to a csv file?
0
gravatar for mictadlo
24 months ago by
mictadlo0
mictadlo0 wrote:

Hi,

How is it possible save the output from glmTreat to a csv file?

> tr <- glmTreat(fit, contrast=B.LvsP, lfc=log2(1.5))
> topTags(tr)
Coefficient:  -1Leaves.2 1Leaves.3

          logFC unshrunk.logFC logCPM  PValue     FDR
sp0090975   2.6            2.6    2.8 5.7e-14 2.7e-09
sp0037632  -3.0           -3.0    3.4 1.7e-13 2.7e-09
sp0074153  -3.9           -3.9    3.8 1.8e-13 2.7e-09
sp0008306   3.2            3.2    2.9 1.8e-13 2.7e-09
sp0073530  -4.5           -4.5    3.4 2.3e-12 2.3e-08
sp0025713  -3.9           -3.9    4.4 2.6e-12 2.3e-08
sp0037721   7.8            8.0    2.4 2.7e-12 2.3e-08
sp0083660   2.0            2.0    4.4 3.2e-12 2.3e-08
sp0052245  -2.9           -2.9    4.9 3.9e-12 2.6e-08
sp0071520  -3.3           -3.3    2.7 5.8e-12 3.4e-08

Thank you in advance.

edger rna-seq • 287 views
ADD COMMENTlink modified 24 months ago by Aaron Lun24k • written 24 months ago by mictadlo0
Answer: Saving output from glmTreat to a csv file?
3
gravatar for Aaron Lun
24 months ago by
Aaron Lun24k
Cambridge, United Kingdom
Aaron Lun24k wrote:

Try using the write.csv function.

library(edgeR)
example(glmTreat)
res <- topTags(tr, n=Inf)
write.csv(file="output.csv", res$table)
ADD COMMENTlink modified 24 months ago by Gordon Smyth38k • written 24 months ago by Aaron Lun24k

By any chance, do you know how it would be possible to create an R named vector where the names are genes and the values are p-values from `tr` without save `tr` to a file?

ADD REPLYlink written 24 months ago by mictadlo0

Use names<- or setNames on res$table$PValue.

ADD REPLYlink written 24 months ago by Aaron Lun24k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 144 users visited in the last hour