Mercurial > repos > artbio > gsc_filter_genes
comparison filter_genes.R @ 1:5d2304b09f58 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_filter_genes commit d9e43e514d5fe7bbc7205a52ccb3e4faef50e856
author | artbio |
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date | Mon, 24 Jun 2019 18:07:05 -0400 |
parents | f689c4ea8c43 |
children | afe949d332b3 |
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0:f689c4ea8c43 | 1:5d2304b09f58 |
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79 kept_genes <- rowSums(data.counts != 0) >= (opt$absolute_detection) | 79 kept_genes <- rowSums(data.counts != 0) >= (opt$absolute_detection) |
80 } | 80 } |
81 | 81 |
82 # Filter matrix | 82 # Filter matrix |
83 data.counts <- data.counts[kept_genes,] | 83 data.counts <- data.counts[kept_genes,] |
84 data.counts <- cbind(Genes=rownames(data.counts), data.counts) | |
84 | 85 |
85 # Save filtered matrix | 86 # Save filtered matrix |
86 write.table( | 87 write.table( |
87 data.counts, | 88 data.counts, |
88 opt$output, | 89 opt$output, |
89 sep = "\t", | 90 sep = "\t", |
90 quote = F, | 91 quote = F, |
91 col.names = T, | 92 col.names = T, |
92 row.names = T | 93 row.names = F |
93 ) | 94 ) |