Mercurial > repos > iuc > scater_filter
comparison scater-manual-filter.R @ 0:e6ca62ac65c6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
author | iuc |
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date | Thu, 18 Jul 2019 11:13:41 -0400 |
parents | |
children | b7ea9f09c02f |
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-1:000000000000 | 0:e6ca62ac65c6 |
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1 #!/usr/bin/env Rscript | |
2 # Manually filter SingleCellExperiment with user-defined parameters | |
3 | |
4 # Load optparse we need to check inputs | |
5 library(optparse) | |
6 library(workflowscriptscommon) | |
7 library(LoomExperiment) | |
8 library(scater) | |
9 | |
10 # parse options | |
11 option_list = list( | |
12 make_option( | |
13 c("-i", "--input-loom"), | |
14 action = "store", | |
15 default = NA, | |
16 type = 'character', | |
17 help = "A SingleCellExperiment object file in Loom format." | |
18 ), | |
19 make_option( | |
20 c("-d", "--detection-limit"), | |
21 action = "store", | |
22 default = 0, | |
23 type = 'numeric', | |
24 help = "Numeric scalar providing the value above which observations are deemed to be expressed" | |
25 ), | |
26 make_option( | |
27 c("-l", "--library-size"), | |
28 action = "store", | |
29 default = 0, | |
30 type = 'numeric', | |
31 help = "Minimum library size (mapped reads) to filter cells on" | |
32 ), | |
33 make_option( | |
34 c("-m", "--percent-counts-MT"), | |
35 action = "store", | |
36 default = 100, | |
37 type = 'numeric', | |
38 help = "Maximum % of mitochondrial genes expressed per cell. Cells that exceed this value will be filtered out." | |
39 ), | |
40 make_option( | |
41 c("-o", "--output-loom"), | |
42 action = "store", | |
43 default = NA, | |
44 type = 'character', | |
45 help = "File name in which to store the SingleCellExperiment object in Loom format." | |
46 ) | |
47 ) | |
48 | |
49 opt <- wsc_parse_args(option_list, mandatory = c('input_loom', 'output_loom')) | |
50 | |
51 # Check parameter values | |
52 | |
53 if ( ! file.exists(opt$input_loom)){ | |
54 stop((paste('File', opt$input_loom, 'does not exist'))) | |
55 } | |
56 | |
57 # Filter out unexpressed features | |
58 | |
59 scle <- import(opt$input_loom, format='loom', type='SingleCellLoomExperiment') | |
60 print(paste("Starting with", ncol(scle), "cells and", nrow(scle), "features.")) | |
61 | |
62 # Create a logical vector of features that are expressed (above detection_limit) | |
63 feature_expressed <- nexprs(scle, detection_limit = opt$detection_limit, exprs_values = 1, byrow=TRUE) > 0 | |
64 scle <- scle[feature_expressed, ] | |
65 | |
66 print(paste("After filtering out unexpressed features: ", ncol(scle), "cells and", nrow(scle), "features.")) | |
67 | |
68 # Filter low library sizes | |
69 to_keep <- scle$total_counts > opt$library_size | |
70 scle <- scle[, to_keep] | |
71 | |
72 print(paste("After filtering out low library counts: ", ncol(scle), "cells and", nrow(scle), "features.")) | |
73 | |
74 # Filter out high MT counts | |
75 to_keep <- scle$pct_counts_MT < opt$percent_counts_MT | |
76 scle <- scle[, to_keep] | |
77 | |
78 print(paste("After filtering out high MT gene counts: ", ncol(scle), "cells and", nrow(scle), "features.")) | |
79 | |
80 # Output to a Loom file | |
81 if (file.exists(opt$output_loom)) { | |
82 file.remove(opt$output_loom) | |
83 } | |
84 export(scle, opt$output_loom, format='loom') |