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Strand Lab
sc-TissueMapper
Commits
127fdb34
Commit
127fdb34
authored
Jan 12, 2019
by
Gervaise Henry
🤠
Browse files
Replace sc_QC parameters as seurat subset has error reading variables inside functions
parent
908e1bbc
Changes
2
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Inline
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r.scripts/sc-TissueMapper_RUN.R
View file @
127fdb34
...
...
@@ -26,13 +26,19 @@ scFolders()
sc10x
<-
scLoad
(
p
=
project.name
)
results
<-
scQC
(
sc10x
,
lg
=
500
,
hg
=
2500
,
hm
=
0.1
,
sub
=
FALSE
)
lg
=
500
hg
=
2500
hm
=
0.1
results
<-
scQC
(
sc10x
,
lg
=
lg
,
hg
=
hg
,
hm
=
hm
,
sub
=
FALSE
)
sc10x
<-
results
[[
1
]]
counts.cell.raw
<-
results
[[
2
]]
counts.gene.raw
<-
results
[[
3
]]
counts.cell.filtered
<-
results
[[
4
]]
counts.gene.filtered
<-
results
[[
5
]]
rm
(
results
)
rm
(
lg
)
rm
(
hg
)
rm
(
hm
)
results
<-
scCellCycle
(
sc10x
,
sub
=
FALSE
)
sc10x
<-
results
[[
1
]]
...
...
r.scripts/sc-TissueMapper_functions.R
View file @
127fdb34
...
...
@@ -146,9 +146,9 @@ scQC <- function(sc10x,lg=500,hg=2500,hm=0.1,sub=FALSE){
counts.gene.raw
<-
nrow
(
GetAssayData
(
object
=
sc10x
,
slot
=
"counts"
))
#Filter/normalize data
sc10x.sub
<-
subset
(
x
=
sc10x
,
subset
=
nFeature_RNA
>
lg
)
sc10x.sub
<-
subset
(
x
=
sc10x.sub
,
subset
=
nFeature_RNA
<
hg
)
sc10x.sub
<-
subset
(
x
=
sc10x.sub
,
subset
=
percent.mito
<
hm
)
sc10x.sub
<-
subset
(
x
=
sc10x
,
subset
=
nFeature_RNA
>
lg
)
sc10x.sub
<-
subset
(
x
=
sc10x.sub
,
subset
=
nFeature_RNA
<
hg
)
sc10x.sub
<-
subset
(
x
=
sc10x.sub
,
subset
=
percent.mito
<
hm
)
sc10x.sub
<-
NormalizeData
(
object
=
sc10x.sub
,
normalization.method
=
"LogNormalize"
,
scale.factor
=
10000
,
verbose
=
FALSE
)
#Plot filtered stats
...
...
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