Question

delete samples from summarizedExperiment

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annkolman78 • 0

@annkolman78-21980

Last seen 6.1 years ago

Hi,

I would like to remove certain numbers of my samples from the rds-summarizedexperiment file. How I can do it using a file contains the samples I want to retain. I can do it with one sample (test = data[, data$SAMPLEID == "451", ) but not sure how I can do it with a list. Thank you for your help.

Anna

deseq2 • 2.1k views

ADD COMMENT • link updated 6.1 years ago by James W. MacDonald 68k • written 6.1 years ago by annkolman78 • 0

score 1 · Answer 1 · 2019-09-24

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James W. MacDonald 68k

@james-w-macdonald-5106

Last seen 3 hours ago

United States

test <- data[,data$SAMPLEID %in% c("451",<other sample IDs go here>)]

ADD COMMENT • link 6.1 years ago James W. MacDonald 68k

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Thank you, it worked, and instead of manually writing all samples ID , can I use a file with all my samples I want to keep? for example: head(samplestostay) SampleID 1 39 2 4 3 6 4 400 5 481 6 500 451

ADD REPLY • link 6.1 years ago annkolman78 • 0

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Yes. You just need a character vector of the IDs you want to keep. There are many ways of doing so, including reading in a file.

ADD REPLY • link 6.1 years ago James W. MacDonald 68k