Question: How can I annotate GRanges object in R with refSeqID, gene symbol, description and entrezID?
1
Tori • 80 wrote:
I have GRanges object which i got from methylKit. It looks like
GRanges with 148 ranges and 2 metadata columns:
seqnames ranges strand | qvalue
<Rle> <IRanges> <Rle> | <numeric>
[1] chr1 [ 1173916, 1174263] * | 9.62686423555631e-08
[2] chr1 [ 2121018, 2121818] * | 0
[3] chr1 [ 7887199, 7887476] * | 0
[4] chr1 [27675920, 27678016] * | 0
[5] chr1 [38461585, 38461988] * | 0
... ... ... ... ... ...
[144] chr9 [140310895, 140312457] * | 0
[145] chrX [ 12601483, 12601832] * | 0
[146] chrX [ 44169511, 44169765] * | 0
[147] chrX [153193514, 153194074] * | 0
[148] chrY [ 13370337, 13370718] * | 0
meth.diff
<numeric>
[1] -18.3771706593283
[2] 17.4420646973258
[3] -27.3603533740319
[4] 23.8514605550414
[5] 22.0042776419856
... ...
[144] 36.7176878762224
[145] 16.0299020341895
[146] 31.7676985330744
[147] 20.503021579582
[148] 16.6634521596941
---
seqlengths:
chr1 chr10 chr11 chr12 chr13 chr14 ... chr6 chr7 chr8 chr9 chrX chrY
NA NA NA NA NA NA ... NA NA NA NA NA NA
How can I annotate it with with refSeqID, gene symbol, description and entrezID?
