Diffbind dba.count doesn’t give FRiP score

Diffbind dba.count doesn’t give FRiP score

1

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?


Diffbind


FRiP

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