Diffbind dba.count doesn’t give FRiP score
Hi I am completely new to DiffBind, R and programming in general. I want to use diffbind to analyze peaks called with macs2. When I use dba.count(), I can not get FRiP score at all. I googled this question, but didn’t work.
Here is the format of sample.csv:
SampleID Replicate bamReads Peaks PeakCaller
Here is the code:
library(DiffBind)
sample1 <- dba(sampleSheet="Z:/sample.csv")
sample1
10 Samples, 931 sites in matrix (15048 total):
ID Replicate Intervals
1 cfDNA21 1 2425
2 cfDNA22 1 2769
3 cfDNA23 1 1887
4 cfDNA24 1 587
5 cfDNA25 1 1269
6 cfDNA26 1 1082
7 cfDNA27 1 994
8 cfDNA28 1 2529
9 cfDNA29 1 2427
10 cfDNA30 1 1637
tam.counts <- dba.count(sample1)
(Sample: Z:/cfDNA30.bam125 Reads will be counted as Paired-end.
Warning messages:1: In serialize(data, node$con) :'package:stats' may not be available when loading)
tam.counts
10 Samples, 443 sites in matrix:
ID Replicate Reads
1 cfDNA21 1 1267699.0
2 cfDNA22 1 751270.0
3 cfDNA23 1 410182.5
4 cfDNA24 1 264162.5
5 cfDNA25 1 239933.0
6 cfDNA26 1 172226.0
7 cfDNA27 1 196008.0
8 cfDNA28 1 753888.5
9 cfDNA29 1 1561326.5
10 cfDNA30 1 340597.0
There is no FRiP column, I dont know why. Someone encountered the same problem, but it was not successfully solved. Can anyone answer this question?
• 32 views
Read more here: Source link