How to generate a rank file from gene expression data in R
Previously I wrote about how to make a gene expression rankfile using the unix shell. While this works for me just fine, there are some differences in the behaviour of shell tools like awk an sed that make it unusable for mac users. Therefore, I think the best solution is to show you how to do this in R, which you can install on Linux, Mac and Windows systems. The expression data for this demo looks like this (the first 5 columns). Name logFC logCPM LR PValue ENSG00000134294.9_SLC38A2 0.365464972841137 8.35504063447063 80.9697378748286 2.29200821312451e-19 ENSG00000164692.13_COL1A2 0.369440969815233 6.9371167845581 59.239238358843 1.39621819298599e-14 ENSG00000117152.9_RGS4 0.417512339007825 6.27805181231213 48.690887963755 2.99655418444362e-12 ENSG00000120738.7_EGR1 -0.448872068345368 5.72373823077344 40.5159113813129 1.95021420597484e-10 ENSG00000236552.1_RPL13AP5 -0.26