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hicPCA using Gene Track #719
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Hi, Thanks for reporting this and providing a patch for this issue. I will consider it in the next release of HiCExplorer. Best, Joachim |
thank @mxw010 for providing a work around, i temporarily solved this problem by adding this skip line edit: |
@mxw010 What reference genome is this? hg19 is bigger, and hg38 matches for the most chromosomes, but chromosomes 4 and X are not correct. (https://hgdownload.cse.ucsc.edu/goldenpath/hg19/bigZips/hg19.chrom.sizes and https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/#/st) For example hg19: For chromosome 1 you have |
@TTTPOB Please provide more information why it fails for you. What reference genome do you use, what are your chromosome sizes, have you used a chromosome size file to create the matrix, and what exact data you use for the correlation? |
(sorry for not providing needed information in time, I am busy with some other project these days |
@joachimwolff the genome.size I used in creating interaction matrix were:
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As mentioned in #716, when correcting for the signs for eigenvectors using a gene track, hicPCA back calculates size of the genome based on bins sometime, instead of the actual size of the chromosomes. For example, in my data, when hicPCA loads the interaction matrix, the size of the chromosomes are:
This is fine for most chromosomes, but chr4 and chrX both have genes out of the range of the chromosomes, resulting in the same error as seen in #716:
Imo, this can simply be fixed by skipping lines from the gene reference file that are out of range, in function correlateEigenvectorWithGeneTrack:
This shouldn't have a big impact on the sign (unless there is a major problem), and would fix the bug.
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