Mercurial > repos > iuc > scater_filter

annotate scater-manual-filter.R @ 3:652923ce664f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 9961b5acbf9081f10e14bc272406b36854fa2924"
author iuc
date Mon, 08 Nov 2021 12:03:34 +0000
parents 7a365ec81b52
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
1 #!/usr/bin/env Rscript
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
2 # Manually filter SingleCellExperiment with user-defined parameters
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
3
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
4 # Load optparse we need to check inputs
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
5 library(optparse)
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
6 library(workflowscriptscommon)
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
7 library(LoomExperiment)
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
8 library(scater)
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
9
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
10 # parse options
2
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
11 option_list <- list(
0
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
12 make_option(
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
13 c("-i", "--input-loom"),
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
14 action = "store",
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
15 default = NA,
2
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
16 type = "character",
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
17 help = "A SingleCellExperiment object file in Loom format"
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
18 ),
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
19 make_option(
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
20 c("-l", "--library-size"),
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
21 action = "store",
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
22 default = 0,
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
23 type = "numeric",
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
24 help = "Minimum library size (mapped reads) to filter cells on"
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
25 ),
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
26 make_option(
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
27 c("-m", "--percent-counts-MT"),
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
28 action = "store",
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
29 default = 100,
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
30 type = "numeric",
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
31 help = "Maximum % of mitochondrial genes expressed per cell. Cells that exceed this value will be filtered out"
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
32 ),
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
33 make_option(
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
34 c("-f", "--expressed-features"),
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
35 action = "store",
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
36 default = 100,
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
37 type = "numeric",
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
38 help = "Remove cells that have less than the given number of expressed features"
0
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
39 ),
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
40 make_option(
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
41 c("-d", "--detection-limit"),
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
42 action = "store",
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
43 default = 0,
2
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
44 type = "numeric",
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
45 help = "Number of reads mapped to a feature above which it to be deemed as expressed"
0
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
46 ),
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
47 make_option(
2
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
48 c("-e", "--min-cells-expressed"),
1
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents: 0
diff changeset
49 action = "store",
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents: 0
diff changeset
50 default = 0,
2
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
51 type = "numeric",
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
52 help = "Remove features that occur in less than the given number of cells"
0
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
53 ),
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
54 make_option(
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
55 c("-o", "--output-loom"),
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
56 action = "store",
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
57 default = NA,
2
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
58 type = "character",
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
59 help = "File name in which to store the SingleCellExperiment object in Loom format"
0
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
60 )
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
61 )
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
62
2
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
63 opt <- wsc_parse_args(option_list, mandatory = c("input_loom", "output_loom"))
0
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
64
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
65 # Check parameter values
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
66
2
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
67 if (! file.exists(opt$input_loom)) {
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
68 stop((paste("File", opt$input_loom, "does not exist")))
0
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
69 }
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
70
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
71 # Filter out unexpressed features
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
72
2
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
73 sce <- import(opt$input_loom, format = "loom", type = "SingleCellLoomExperiment")
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
74 print(paste("Starting with", ncol(sce), "cells and", nrow(sce), "features."))
0
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
75
2
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
76 # Filter out low quality cells
0
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
77
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
78 # Filter low library sizes
2
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
79 passing_total <- sce$total > opt$library_size
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
80 sce <- sce[, passing_total]
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
81 print(paste("After filtering out low library counts: ", ncol(sce), "cells and", nrow(sce), "features."))
1
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents: 0
diff changeset
82
0
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
83 # Filter out high MT counts
2
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
84 passing_mt_counts <- sce$subsets_Mito_percent < opt$percent_counts_MT
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
85 sce <- sce[, passing_mt_counts]
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
86 print(paste("After filtering out high MT gene counts: ", ncol(sce), "cells and", nrow(sce), "features."))
0
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
87
2
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
88 expr_features <- sce$detected > opt$expressed_features
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
89 sce <- sce[, expr_features]
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
90 print(paste("After filtering out cells with low feature counts: ", ncol(sce), "cells and", nrow(sce), "features."))
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
91
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
92 # Create a logical vector of features that are expressed (above detection_limit)
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
93 feature_expressed <- nexprs(sce, detection_limit = opt$detection_limit, byrow = TRUE) > opt$min_cells_expressed
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
94 sce <- sce[feature_expressed, ]
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
95 print(paste("After filtering out rare features: ", ncol(sce), "cells and", nrow(sce), "features."))
0
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
96
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
97 # Output to a Loom file
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
98 if (file.exists(opt$output_loom)) {
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
99 file.remove(opt$output_loom)
e6ca62ac65c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff changeset
100 }
2
7a365ec81b52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
parents: 1
diff changeset
101 export(sce, opt$output_loom, format = "loom")