Showing posts from April, 2016

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  -0.263118776572713  7.87437056…