ChIPQC Error: subscript contains out-of-bounds ranges
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jkim622 • 0
@jkim622-14752
Last seen 4.6 years ago

Hello,

I am new to using R and ChIP-seq analysis and I was having trouble generating ChIPQC report and hoping if anyone can help me trouble shoot this.

so what I did so far is 

source("http://bioconductor.org/biocLite.R")
biocLite("BiocParallel")

biocLite("ChIPQC")

library(ChIPQC)
library(BiocParallel)
register(SerialParam())

> samples <- read.csv('jkim622_chipseq/meta/ChIPQC.csv')
> View(samples)
> chipObj <- ChIPQC(samples, annotation="hg19", chromosomes = NULL)

And below is what I got along with the error message at the end


E_Veh_1 MCF7 ERa 40min  1 narrow
E_Veh_2 MCF7 ERa 40min  2 narrow
E_Veh_3 MCF7 ERa 40min  3 narrow
E_2_1 MCF7 ERa 40min  1 narrow
E_2_2 MCF7 ERa 40min  2 narrow
E_2_3 MCF7 ERa 40min  3 narrow
E_3_1 MCF7 ERa 40min  1 narrow
E_3_2 MCF7 ERa 40min  2 narrow
E_3_3 MCF7 ERa 40min  3 narrow
E_4_1 MCF7 ERa 40min  1 narrow
E_4_2 MCF7 ERa 40min  2 narrow
E_4_3 MCF7 ERa 40min  3 narrow
Compiling annotation...
Using default blacklist for hg19...
Computing metrics for 24 samples...
list
Bam file has 195 contigs
Calculating coverage histogram for chr1

Calculating SSD for chr1

Calculating unique positions per strand for chr1

Calculating shift for chr1

 300 / 300
Counting reads in features for chr1

Signal over peaks for chr1

done
Calculating coverage
Calculating coverage histogram for chr2

Calculating SSD for chr2

Calculating unique positions per strand for chr2

Calculating shift for chr2

 300 / 300
Counting reads in features for chr2

Signal over peaks for chr2

done
Calculating coverage
Calculating coverage histogram for chr3

Calculating SSD for chr3

Calculating unique positions per strand for chr3

Calculating shift for chr3

 300 / 300
Counting reads in features for chr3

Signal over peaks for chr3

done
Calculating coverage
Calculating Summits on  chr3  ..Calculating coverage histogram for chr4

Calculating SSD for chr4

Calculating unique positions per strand for chr4

Calculating shift for chr4

 300 / 300
Error: subscript contains out-of-bounds ranges
In addition: Warning messages:
1: In if is.na(peaks)) peaks = NULL :
  the condition has length > 1 and only the first element will be used
2: In if is.na(blacklist)) blacklist = NULL :
  the condition has length > 1 and only the first element will be used

Can someone tell me why I get an error? Also, how do I fix this?

Thank you all in advance for your help!

Ji

 

R • 490 views
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Entering edit mode

I know this is 4.5 years old. I encountered this problem because I had used hg38 to align my reads and I was using hg19 in thr CHIPQC() method. so changing the annotation to hg38 is the solution

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