Question

Subsetting Range Summarized Experiment

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Bine ▴ 50

@bine-23912

Last seen 6 months ago

UK

Dear all,

I am trying to subset my RangeSummarizedExperiment with se[, se$name == lung]. However, when doing so I keep getting this error: Error: logical subscript contains NAs

Does anyone has an idea how I can subset it nevertheless?

Thank you & Best Regards, Bine

SummarizedExperiment • 1.5k views

ADD COMMENT • link 13 months ago Bine ▴ 50

score 2 · Accepted Answer · 2023-10-17

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 22 hours ago

United States

You almost surely don't want to use lung, but instead "lung". In the former, you are saying that there is an object in your workspace called lung that contains the things you want to filter on. In the latter, you are saying that some of the rows in your colData object have "lung" in the name column, and you want to select those columns of your SummarizedExperiment object. In addition, you probably don't want to use equality == in this situation, but instead you want %in%, which is resistant to the existence of NA in your se$name column.

se.small <- se[,se$name %in% "lung"]

ADD COMMENT • link 13 months ago James W. MacDonald 67k

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Hi James,

thanks for your answer. Sorry I forget the " " around lung in the post here, but did put it in my code. It is working now with %in%, that's great, thank you!

Can I ask you one other related question to subsetting of a Summarised Object - I would like to get rid of a column ("primary,site") in colData, but it seems not to work the usual way...

se.small[ , -which(names(se.small) %in% c("primary.site"))]

Do you know how I could do this?

Thank you, Bine

ADD REPLY • link 13 months ago Bine ▴ 50

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se.small[,!se.small$names %in% "primary.site"]

ADD REPLY • link 13 months ago James W. MacDonald 67k

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Thank you. But like this it removes all the values and everything is 0.

I should also mention that the structure is as below for this variable of colData:

Primary.site

Primary.site is a list.

Thank you!!!

ADD REPLY • link 13 months ago Bine ▴ 50

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Rereading your previous post, it's not clear if you want to get rid of a particular column of your colData slot, or if you want to filter on things that are in that column (which apparently is called 'primary_site', rather than 'primary.site').

If the former, you just replace the colData.

colData(se.small) <- colData(se.small)[, !names(colData(se.small)) %in% "primary_site"]

Or if it's as you seem to imply, that you don't want any of the values in se.small$names to be in any of the list items for primary_site, then you can use sapply

nam <- se.small$names
ind <- sapply(se.small$primary_site, function(x) any(x %in% nam))
se.small <- se.small[,!ind]

ADD REPLY • link 13 months ago James W. MacDonald 67k

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Yes, I just wanted to get rid of that column in colData, it worked with colData(se.small) <- colData(se.small)[, !names(colData(se.small)) %in% "primary_site"].

Thanks a lot !

ADD REPLY • link 13 months ago Bine ▴ 50