Mercurial > repos > gaelcge > r_signac_galaxy
comparison signac-subset.R @ 0:6e0b320d8b6a draft default tip
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
author | gaelcge |
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date | Tue, 02 Aug 2022 19:11:27 +0000 |
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-1:000000000000 | 0:6e0b320d8b6a |
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1 #!/usr/bin/env Rscript | |
2 | |
3 # Load optparse we need to check inputs | |
4 | |
5 suppressPackageStartupMessages(require(optparse)) | |
6 | |
7 # Load common functions | |
8 | |
9 suppressPackageStartupMessages(require(workflowscriptscommon)) | |
10 | |
11 # parse options | |
12 | |
13 option_list = list( | |
14 make_option( | |
15 c("--signac-object"), | |
16 action = "store", | |
17 default = NA, | |
18 type = 'character', | |
19 help = "" | |
20 ), | |
21 make_option( | |
22 c("--peak-region-fragments-min"), | |
23 action = "store", | |
24 default = NA, | |
25 type = 'character', | |
26 help = "." | |
27 ), | |
28 make_option( | |
29 c("--peak-region-fragments-max"), | |
30 action = "store", | |
31 default = NA, | |
32 type = 'character', | |
33 help = "." | |
34 ), | |
35 make_option( | |
36 c("--pct-reads-in-peaks"), | |
37 action = "store", | |
38 default = NA, | |
39 type = 'character', | |
40 help = "." | |
41 ), | |
42 make_option( | |
43 c("--blacklist-ratio"), | |
44 action = "store", | |
45 default = NA, | |
46 type = 'character', | |
47 help = "." | |
48 ), | |
49 make_option( | |
50 c("--nucleosome-signal"), | |
51 action = "store", | |
52 default = NA, | |
53 type = 'character', | |
54 help = "." | |
55 ), | |
56 make_option( | |
57 c("--tss-enrichment"), | |
58 action = "store", | |
59 default = NA, | |
60 type = 'character', | |
61 help = "." | |
62 ), | |
63 make_option( | |
64 c("--output-object-file"), | |
65 action = "store", | |
66 default = NA, | |
67 type = 'character', | |
68 help = "File name in which to store serialized R matrix object." | |
69 ) | |
70 ) | |
71 | |
72 opt <- wsc_parse_args(option_list) | |
73 | |
74 suppressPackageStartupMessages(require(Signac)) | |
75 | |
76 # extract gene annotations from EnsDb | |
77 signac_object <- readRDS(file = opt$signac_object) | |
78 | |
79 | |
80 ## transform input parameters to numeric | |
81 peak_region_fragments_min <- as.numeric(opt$peak_region_fragments_min) | |
82 peak_region_fragments_max <- as.numeric(opt$peak_region_fragments_max) | |
83 pct_reads_in_peaks_var <- as.numeric(opt$pct_reads_in_peaks) | |
84 blacklist_ratio_var <- as.numeric(opt$blacklist_ratio) | |
85 nucleosome_signal_var <- as.numeric(opt$nucleosome_signal) | |
86 tss_enrichment_var <- as.numeric(opt$tss_enrichment) | |
87 | |
88 print("Signac object before filtering:") | |
89 | |
90 signac_object | |
91 | |
92 signac_object <- subset(signac_object, peak_region_fragments > peak_region_fragments_min) | |
93 signac_object <- subset(signac_object, peak_region_fragments < peak_region_fragments_max) | |
94 signac_object <- subset(signac_object, pct_reads_in_peaks > pct_reads_in_peaks_var) | |
95 signac_object <- subset(signac_object, blacklist_ratio < blacklist_ratio_var) | |
96 signac_object <- subset(signac_object, nucleosome_signal < nucleosome_signal_var) | |
97 signac_object <- subset(signac_object, TSS.enrichment > tss_enrichment_var) | |
98 | |
99 print("Signac object after filtering:") | |
100 | |
101 signac_object | |
102 | |
103 # Output to a serialized R object | |
104 saveRDS(signac_object, file = opt$output_object_file) |