How to select columns from the dataframe based on variables from another dataframe
I have a dataframe in which each column is microarray data of a sample. I want to select columns based on another dataframe (df2). I was trying to do it using select function of dplyr but somehow it does not work.
df1
>head(df1)
probeID WT.GS1 WT.GS2 WT.GS3 KO.GS1 KO.GS2 KO.GS3
100001_at 11.5 5.6 69.1 15.7 36.0 42.0
100002_at 20.5 32.4 93.3 31.8 14.4 22.9
100003_at 72.4 89.0 79.2 80.5 130.1 86.7
......
df2
>head(df2)
Header SampleType
1 KO.GS1 AR.R
2 KO.GS2 AR.R
3 WT.GS1 AR.R
4 WT.GS2 BL.PD
5 WT.GS3 BL.PD
Let's say I want to select columns from the df1 which match with variables in df2$Header. I was trying to:
>df1 %>% select(dput(as.character(df2$Header)))
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Thanks!! I am looking into SummarizedExperiment. Using dplyr:
>df1 %>% select(one_of(dput(as.character(df2$Header))))
or
>list.df2 <- dput(as.character(df2$Header))
>df1 %>% select(one_of(list.df2))
worked
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Have a look at the examples section of the documentation of the
selectfunction, you will see how to useone_ofto solve your problem. By the way, you may be interested in the SummarizedExperiment objects from Bioconductor, with which you can bind together the data (df1in your example) and the metadata (df2in your example).