Hello, I'm working with R and have obtained a table which contains 3 columns and a row for each of my genes in an RNA-seq study. The first two columns contain fold conc and log fold change, respectively, but I'm most interested in the third column and finding how many of the genes have a p.value less than 0.05. Also bonus points if you can tell me how to count genes with p-value < 0.05 and logFC > 1.
So can anyone help me write some lines in R which will count the number of genes with values less than 0.05 in the third column? Also my data is in a matrix table.
Thanks so much
(here is an illustration what I'm working with)
> head(edgeHSMvHSF$table) logConc logFC p.value tag.1 -13.67186 -0.009198564 0.9914611 tag.2 -36.72240 -26.587301949 1.0000000 tag.3 -15.82522 0.272339616 0.6033744 tag.4 -15.35435 -0.253093387 0.6161544 tag.5 -18.13806 -0.079021620 1.0000000 tag.6 -15.43403 0.868789217 0.0904064
sorry looks like those numbers won't format well here