Question

Could not find function "Standard Chromosomes"

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Entering edit mode

sarah.jobbins • 0

@17027852

Last seen 13 months ago

United States

Hi I'm trying to add ATAC seq to my matrix that already contains scRNAseq data.

The code I'm trying to run is below. The first line works, the second does not. If someone can help me figure out what is going on that would be great. I'm very new to code so any help is appreciated!

grange.counts <- StringToGRanges(rownames(atac_counts), sep = c(":", "-"))
grange.use <- seqnames(grange.counts) %in% standardChromosomes(grange.counts)

# Error in standardChromosomes(grange.counts) : 
  could not find function "standardChromosomes"

scrna scRNAseq • 668 views

ADD COMMENT • link updated 6 months ago by Gabriella • 0 • written 13 months ago by sarah.jobbins • 0

score 0 · Answer 1 · 2023-03-07

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Entering edit mode

James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 15 hours ago

United States

You want

grange.use <- keepStandardChromosomes(grange.counts, pruning.mode = "coarse")

ADD COMMENT • link 13 months ago James W. MacDonald 65k

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Hi,

I had the same problem, and I was able to solve it doing this:

You should install the "GenomeInfoDb" package (BiocManager::install('GenomeInfoDb'))
Load the library
After that you will be able to run grange.use <- seqnames(grange.counts) %in% standardChromosomes(grange.counts)

ADD REPLY • link 6 months ago Gabriella • 0