how to change the format of file in R
I want to change the format of file from input to output (this is just an example of my data)
Input:
head(cpg_region2)
cds downstream exon1 exons intron1 introns other promoter UTR3 UTR5
1 1_47963035 1_68276036 1_47963035 1_47963035 1_33831751 1_33831751 1_32347715 1_48132522 11_18394188 1_68276036
2 1_48088881 10_2648462 1_104414426 1_48088881 1_33831751 1_33831751 14_2527831 1_68276036 11_18394188 12_3142614
3 1_168677980 12_396767 1_168677980 1_68276036 1_34481401 1_33831751 15_7112579 1_70154145 12_3134049 2_120841166
4 10_2627156 14_12686663 12_3142614 1_104414426 1_48132522 1_33831751 17_10524429 1_70154145 13_9959153 20_13434035
5 10_2627156 14_12686663 14_3960061 1_168677980 1_68276036 1_33831751 19_7740157 1_104414426 13_9959153 26_663159
6 10_2627156 15_7007155 17_11003840 10_2627156 1_68276036 1_34188568 2_5702062 1_104414426 16_2178551 26_663159
Output
cds downstream exon1 exons intron1 introns other promoter UTR3 UTR5
1_47963035 1 0 1 1 0 0 0 0 0 0
1_48088881 1 0 0 0 0 0 0 0 0 0
1_68276036 0 1 0 0 0 0 0 0 0 0
.
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2 answers
It's basically the same as here: how to make a UpSet plot with data frame in R
Reshape from wide-to-long - stack, then use table to get the counts:
as.data.frame.matrix(table(stack(cpg_region2)))
# cds downstream exon1 exons intron1 introns other promoter UTR3 UTR5
#1_104414426 0 0 1 1 0 0 0 2 0 0
#1_168677980 1 0 1 1 0 0 0 0 0 0
#1_32347715 0 0 0 0 0 0 1 0 0 0
#1_33831751 0 0 0 0 2 5 0 0 0 0
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