I am trying to replicate the format of the below file, which seems to include both the raw counts AND the DESeq data into one csv
WTS1 WTS2 KOS1 KOS2 baseMean log2FoldChange lfcSE stat pvalue padj
Gm6166 10 20 4103 4166 1931.08 5.93 0.13 45.68 0.00e+00 0.00e+00
TNFa 8492 10719 1091 1158 5621.18
However, I can't seem to figure out how to do it with the two separate counts.csv
WT_S1_12hr WT_S2_12hr KO_S1_12hr KO_S2_12hr
0610005C13Rik 1 0 2 1
0610006L08Rik 0 0 0 0
and deseq data (below).
baseMean log2FoldChange lfcSE stat pvalue padj
0610009B22Rik 261.0242 0.0652558 0.1773184 0.368015 0.712862 0.908775
0610009L18Rik 26.6356 -0.4974079 0.5355241 -0.928825 0.352980 NA
I know how to combine annotation files and counts files, but not this kind of data.
Would someone be willing to show me how to do this?
•
written
by
cdeantoneo31 •
3 answers
you can use the paste command to place join files line by line. For it work the files must be in the exact same order
$ cat a
1
2
3
$ cat b
A
B
C
$ paste a b
1 A
2 B
3 C
To cut out some columns from the results use the cut command.
$ paste a b a b a b a b | cut -f 1-3,5-7
1 A 1 1 A 1
2 B 2 2 B 2
3 C 3 3 C 3
If the files are not in order or the number of lines differ you would need to use join plus some other prior steps.
If you want to do it within R, if you have both files as data.frames, you can do, for each of the columns (the files do not need to be in the same order, however they should have the same genes in order to avoid NAs)
# Convert to dataframes if they are matrices
dataframe_deseq2 <- as.data.frame(dataframe_deseq2)
dataframe_counts <- as.data.frame(dataframe_counts)
# Do this for each column you want to add
dataframe_deseq2$WT_S1_12hr <- dataframe_counts$WT_S1_12hr[match(rownames(dataframe_deseq2),rownames(dataframe_counts))]
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