Question

ChIPpeakAnno can not load data

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文杰 • 0

@a4dfd057

Last seen 2 days ago

Taiwan

>macs_peak <- system.file("extdata", 'H820_OsiR_1_peaks.xls', package = "ChIPpeakAnno")`
> macs_peak

[1] ""

> macs_peak_gr <- toGRanges(macs_peak, format = "MACS")
Error in read.table(data, header = header, comment.char = comment.char,  :

system.file can not work

genomes ChIPpeakAnno • 90 views

ADD COMMENT • link updated 2 days ago by hukai916 ▴ 10 • written 2 days ago by 文杰 • 0

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Where is there a reference to this file? Indeed this file does not exist in this package.

ADD REPLY • link 2 days ago shepherl 4.0k

score 0 · Answer 1 · 2024-09-17

ChIPpeakAnno stores several example files under its extdata directory for demonstration purposes. These files can be found with the system.file() function. That being said, if the file (e.g. "H820_OsiR_1_peaks.xls") is not pre-existing in the package, system.file() will not find it. A side note, you have an extra backtick ("`") at the end of your first commend.