Mercurial > repos > iuc > dropletutils

comparison scripts/dropletutils.Rscript @ 5:d5e4b59d5331 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ea9a67b5711b53fb911a0c50b6b49eb9db2366a7"
author iuc
date Wed, 29 Jan 2020 20:07:15 +0000
parents 2bbf0052aaa9
children a79cf05ca77d
comparison
equal deleted inserted replaced
4:a75b34ff05f0 5:d5e4b59d5331
32 32
33 writeOut <- function(object, fileout, typeout){ 33 writeOut <- function(object, fileout, typeout){
34 if (typeout == "tsv"){ 34 if (typeout == "tsv"){
35 writeTSV(fileout, getCounts(object)) 35 writeTSV(fileout, getCounts(object))
36 } 36 }
37 else if (typeout == "h5ad"){ 37 else if (typeout == "h5"){
38 write10xCounts(fileout, getCounts(object), 38 write10xCounts(fileout, getCounts(object),
39 type="HDF5", 39 type="HDF5",
40 gene.symbol=determineGeneIDs(object), 40 gene.symbol=determineGeneIDs(object),
41 overwrite=TRUE) 41 overwrite=TRUE)
42 } 42 }
53 if (typein == "tsv"){ 53 if (typein == "tsv"){
54 ## Exploding memory problems occured here 54 ## Exploding memory problems occured here
55 ## - solution is to use the readSparseCounts function from scater 55 ## - solution is to use the readSparseCounts function from scater
56 sce <- SingleCellExperiment(assays = list(counts = readSparseCounts(filein))) 56 sce <- SingleCellExperiment(assays = list(counts = readSparseCounts(filein)))
57 } 57 }
58 else if (typein == "h5ad"){ 58 else if (typein == "h5"){
59 sce <- read10xCounts(filein, col.names=T, type="HDF5") # use barcodes.tsv as column names 59 sce <- read10xCounts(filein, col.names=T, type="HDF5") # use barcodes.tsv as column names
60 } 60 }
61 else if (typein == "directory"){ 61 else if (typein == "directory"){
62 sce <- read10xCounts(filein, col.names=T, type="sparse") 62 sce <- read10xCounts(filein, col.names=T, type="sparse")
63 } 63 }
67 67
68 68
69 ## Methods 69 ## Methods
70 70
71 71
72 doEmptyDrops <- function(files, eparams, in.type="directory", out.type="h5ad", fdr_threshold = 0.01){ 72 doEmptyDrops <- function(files, eparams, in.type="directory", out.type="h5", fdr_threshold = 0.01){
73 sce <- read10xFiles(files$infile, in.type) 73 sce <- read10xFiles(files$infile, in.type)
74 74
75 eparams$... <- NULL ## hack 75 eparams$... <- NULL ## hack
76 eparams$m = Matrix(counts(sce), sparse=TRUE) 76 eparams$m = Matrix(counts(sce), sparse=TRUE)
77 77
113 message(paste("Cells:", sum(na.omit(e.out$is.Cell)))) 113 message(paste("Cells:", sum(na.omit(e.out$is.Cell))))
114 message(paste("Cells and Limited:", sum(na.omit(e.out$is.CellAndLimited)))) 114 message(paste("Cells and Limited:", sum(na.omit(e.out$is.CellAndLimited))))
115 } 115 }
116 116
117 117
118 doDefaultDrops <- function(files, dparams, in.type="directory", out.type="h5ad"){ 118 doDefaultDrops <- function(files, dparams, in.type="directory", out.type="h5"){
119 sce <- read10xFiles(files$infile, in.type) 119 sce <- read10xFiles(files$infile, in.type)
120 120
121 dparams$m = counts(sce) 121 dparams$m = counts(sce)
122 called <- do.call(defaultDrops, c(dparams)) 122 called <- do.call(defaultDrops, c(dparams))
123 123