search

YuLab-SMU / ChIPseeker

:dart: ChIP peak Annotation, Comparison and Visualization
https://onlinelibrary.wiley.com/share/author/GYJGUBYCTRMYJFN2JFZZ?target=10.1002/cpz1.585
220 stars 74 forks source link

RAM usage question for getTagMatrix and plotAvgProf using GFF txdb #145

Closed MrKevinDC closed 2 years ago

MrKevinDC commented 3 years ago

Hi, I have required 100 GB of RAM to be able to run:

txdb <- makeTxDbFromGFF(opt$knownGenes)
promoter <- getPromoters(TxDb=txdb, upstream=3000, downstream=3000)
tagMatrix <- getTagMatrix(peakFiles[[1]], windows=promoter)
plotAvgProf(tagMatrix, xlim=c(-3000, 3000), conf = 0.95, resample = 1000)

And its tagMatrixList variations. My input files are UCSC's hg38 knownGenes GFF (size of 312MB) and peak files of a narrowPeak format with a size of 600KB. Is this expected?

GuangchuangYu commented 2 years ago

These two PRs, https://github.com/YuLab-SMU/ChIPseeker/pull/147 and https://github.com/YuLab-SMU/ChIPseeker/pull/156, should solve this issue.