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Strand Lab
sc-TissueMapper
Commits
730114a6
Commit
730114a6
authored
Feb 27, 2019
by
Gervaise Henry
🤠
Browse files
Fix aggregation.csv file load for cellranger 3
parent
e11be2da
Changes
1
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Inline
Side-by-side
r.scripts/sc-TissueMapper_functions.R
View file @
730114a6
...
...
@@ -53,9 +53,17 @@ scLoad <- function(p,mc=3,mg=200,sub=FALSE,cellranger=3,ref="GRCh38"){
#Label sample names from aggregation_csv.csv
if
(
sub
==
FALSE
){
sc10x.aggr
<-
read_csv
(
"./analysis/DATA/10x/aggregation_csv.csv"
)
if
(
cellranger
==
2
){
sc10x.aggr
<-
read_csv
(
"./analysis/DATA/10x/aggregation_csv.csv"
)
}
else
{
sc10x.aggr
<-
read_csv
(
"./analysis/DATA/10x/aggregation.csv"
)
}
}
else
{
sc10x.aggr
<-
read_csv
(
paste0
(
"./analysis/DATA/"
,
p
,
"/10x/aggregation_csv.csv"
))
if
(
cellranger
==
2
){
sc10x.aggr
<-
read_csv
(
paste0
(
"./analysis/DATA/"
,
p
,
"/10x/aggregation_csv.csv"
))
}
else
{
sc10x.aggr
<-
read_csv
(
paste0
(
"./analysis/DATA/"
,
p
,
"/10x/aggregation.csv"
))
}
}
cell.codes
<-
as.data.frame
(
sc10x
@
raw.data
@
Dimnames
[[
2
]])
colnames
(
cell.codes
)
<-
"barcodes"
...
...
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