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Bastien Hervé
Delete custom additional column from Seurat metadata
I add some columns of custom metadata by using the Seurat v3.X command object$name <- vector, but I can't delete these columns, such as "time", "hours". I try many many ways, like subset, subsetdata, and test.tc11$hours <- NULL, all them didn't work.
Can you help me?
> test.tc11$hours <- rep("E14",7303)
> tail(x = test.tc11[[]])
orig.ident nCount_RNA nFeature_RNA percent.mito RNA_snn_res.0.8 letter.idents time DAY hours
A_TTTGTCACATTGGTAC SeuratProject 3987 1775 0 7 H E11 E14 E14
A_TTTGTCAGTAAGTGGC SeuratProject 4299 1992 0 7 H E11 E14 E14
A_TTTGTCAGTAGGACAC SeuratProject 6994 2448 0 0 A E11 E14 E14
A_TTTGTCAGTAGGCATG SeuratProject 7906 2588 0 4 E E11 E14 E14
A_TTTGTCAGTCTCATCC SeuratProject 24778 5035 0 8 I E11 E14 E14
A_TTTGTCAGTTCTGTTT SeuratProject 8209 2628 0 2 C E11 E14 E14
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Friederike
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yuhongruoyi •
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yuhongruoyi •
2 answers
this worked for me:
> test_seur$testing <- "testing"
> str(test_seur@meta.data)
'data.frame': 979 obs. of 4 variables:
$ orig.ident : chr "AdultHS" "AdultHS" "AdultHS" "AdultHS" ...
$ nCount_RNA : num NA NA NA NA NA NA NA NA NA NA ...
$ nFeature_RNA: int NA NA NA NA NA NA NA NA NA NA ...
$ testing : chr "testing" "testing" "testing" "testing" ...
> test_seur@meta.data$testing <- NULL
> str(test_seur@meta.data)
'data.frame': 979 obs. of 3 variables:
$ orig.ident : chr "AdultHS" "AdultHS" "AdultHS" "AdultHS" ...
$ nCount_RNA : num NA NA NA NA NA NA NA NA NA NA ...
$ nFeature_RNA: int NA NA NA NA NA NA NA NA NA NA ...
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Friederike
If Seurat output object class is a data.frame then any of the below should work:
# check class
class(mtcars)
# [1] "data.frame"
# assign NULL
mtcars$cyl <- NULL
# remove by match on name
mtcars <- mtcars[, -match("cyl", colnames(mtcars)) ]
# remove by index
mtcars <- mtcars[, -2 ]
See SO posts for alternatives here and here.
Check the output of str(mydata), class(mydata), and provide reproducible example: dput(head(mydata)).
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