Delete custom additional column from Seurat metadata

Question

[yuhongruoyi]

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

[Bastien Hervé]

df <- df[,-c($column_number)] ?

Answer 1

[Friederike]

this worked for me:

> test_seur$testing <- "testing"
> str([e-mail])
'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" ...
> [e-mail]$testing <- NULL
> str([e-mail])
'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 ...

Answer 2

[zx8754]

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)).