Hi,
I have a Differential expressed genes with edgeR in dataframe "er"
X logFC logCPM F PValue FDR
LYVE1 -2.286965927 3.622301526 15.20371163 9.69E-05 0.013364458
LANCL2 -2.211422717 5.037579176 41.62021204 1.17E-10 2.65E-07
MRPL37 -2.100712376 7.077497716 33.64633822 6.82E-08 6.53E-05
ARHGDIB -2.075307337 2.263760868 12.39278702 0.000432777 0.034317014
SNORA57 -1.976169985 2.843788903 14.92295881 0.000112552 0.014418635
C14orf105 -1.859401694 3.004499365 13.02450243 0.000308388 0.028440396
ATP2B2 1.922575077 3.836340714 21.03069806 4.55E-06 0.001679724
ACSM3 1.915862102 3.268232386 14.04761306 0.000178872 0.019977015
UNC93A 1.914557961 2.779896967 12.53269014 0.000401039 0.033134889
TFR2 1.897779698 2.734046964 11.91293895 0.000558906 0.039911789
ABCA2 1.875311985 4.024932749 22.0241006 2.71E-06 0.0011637
NTS 1.859274971 6.165644757 17.75363345 2.53E-05 0.005418355
DLK1 1.849908433 6.965559508 18.95639802 1.35E-05 0.003334802
FAM171A2 1.845821788 2.878346297 14.4304531 0.000145974 0.017022099
SLC26A1 1.817559593 2.926690164 13.39813378 0.000253075 0.024793914
Using the above table based on logFC and PValue I ranked the genes.
er$fcsign <- sign(er$logFC)
er$logP=-log10(er$PValue)
er$metric= er$logP/er$fcsign
final<-er[,c("X", "metric")]
head(final)
X metric
LYVE1 -4.0136762
LANCL2 -9.9318141
MRPL37 -7.1662156
ARHGDIB -3.3637358
SNORA57 -3.9486468
C14orf105 -3.5109025
ATP2B2 5.341988603
ACSM3 3.747457637
UNC93A 3.396813391
TFR2 3.252661228
ABCA2 5.567030709
NTS 4.596879479
DLK1 4.869666232
FAM171A2 3.835724491
SLC26A1 3.596750754
Now with the available hallmark pathways file h.all.v6.2.symbols.gmt
I would like to run GSEA on the list and want the whole pathways output. Not only significant pathways.
can anyone tell how to do that.