I've been trying to solve this problem for a while now and I can't figure it out. I'm trying to run DiffBind on ATACseq samples I have and keep getting the following error after trying to create the dba:
line13 <- dba(sampleSheet="/home/nalewis/13lineATACseq/DiffBind/XIII_Line_Sheet.csv")
N13P1 DIPGK27M None Mut none 1 bed
N13P2 DIPGK27M None Mut none 2 bed
N13W1 DIPGWT None WT none 1 bed
N13W2 DIPGWT None WT none 2 bed
Error in if (res >= minval) { : missing value where TRUE/FALSE needed
I've tried setting the minOverlap=2 and that did not solve my problem. I think the csv is fine because it reads my table just fine (see below for reference). It's just when I try to create the dba object that it suddenly throws an error at me and I haven't found a solution anywhere.
samples <- read.csv("/home/nalewis/13lineATACseq/DiffBind/XIII_Line_Sheet.csv")
> names(samples)
[1] "SampleID" "Tissue" "Factor" "Condition" "Treatment"
[6] "Replicate" "bamReads" "Peaks" "PeakCaller" "PeakFormat"
[11] "ScoreCol" "LowerBetter"
samples
SampleID Tissue Factor Condition Treatment Replicate
1 N13P1 DIPGK27M None Mut none 1
2 N13P2 DIPGK27M None Mut none 2
3 N13W1 DIPGWT None WT none 1
4 N13W2 DIPGWT None WT none 2
bamReads
1 /home/nalewis/13lineATACseq/alignment/N13P1/noM_N13P1.bam
2 /home/nalewis/13lineATACseq/alignment/N13P2/noM_N13P2.bam
3 /home/nalewis/13lineATACseq/alignment/N13W1/noM_N13W1.bam
4 /home/nalewis/13lineATACseq/alignment/N13W2/noM_N13W2.bam
Peaks PeakCaller PeakFormat
1 /home/nalewis/13lineATACseq/peaks/N13P1/N13P1peaks.bed bed bed
2 /home/nalewis/13lineATACseq/peaks/N13P2/N13P2peaks.bed bed bed
3 /home/nalewis/13lineATACseq/peaks/N13W1/N13W1peaks.bed bed bed
4 /home/nalewis/13lineATACseq/peaks/N13W2/N13W2peaks.bed bed bed
ScoreCol LowerBetter
1 5 FALSE
2 5 FALSE
3 5 FALSE
4 5 FALSE
What version of
DiffBind
are you running?I have bioconductor-diffbind version 1.16.3 through the build channel bioconda.
Wow, are you sure? That is five years old and definitely no longer supported. What version of R are you running? Could you post the output of sessionInfo()?
I have R 3.2.2. I was having issues checking the version of DiffBind the way the bioconductor website tells you to do it so I have gone to wrong place or entered the wrong code. I'm very new to coding so I'm still learning the ropes with all this. Here is the output from sessionInfo():
sessionInfo()