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Strand Lab
sc-TissueMapper
Commits
dbb4d204
Commit
dbb4d204
authored
Feb 16, 2020
by
Gervaise Henry
🤠
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Change threshold code to match qc thresh
parent
7e720ca8
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r.scripts/sc-TissueMapper_functions.R
r.scripts/sc-TissueMapper_functions.R
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r.scripts/sc-TissueMapper_functions.R
View file @
dbb4d204
...
...
@@ -717,7 +717,7 @@ scScore <- function(sc10x,score,geneset,cut.pt=0.9,anchor=FALSE){
h
<-
hist
(
data.frame
(
sc10x
[[
paste0
(
score
,
"1"
)]])[,
paste0
(
score
,
"1"
)],
breaks
=
1000
,
plot
=
FALSE
)
cutoff.temp
<-
mean
(
c
(
h
$
mids
[
which.max
(
h
$
counts
)],
h
$
mids
[
-
which.max
(
h
$
counts
)][
which.max
(
h
$
counts
[
-
which.max
(
h
$
counts
)])]))
cells.remove
<-
rownames
(
sc10x
[[
paste0
(
score
,
"1"
)]])[
sc10x
[[
paste0
(
score
,
"1"
)]][,
1
]
<
cutoff.temp
]
sc10x.temp
<-
subset
(
sc10x
,
cells
=
setdiff
(
colnames
(
sc10x
),
cells.remove
)
)
sc10x.temp
<-
subset
(
sc10x
,
cells
=
cells.remove
,
invert
=
TRUE
)
thresh
<-
list
()
thresh
[[
"all"
]]
<-
scThresh
(
list
(
all
=
sc10x.temp
),
feature
=
paste0
(
score
,
"1"
),
sub
=
score
)
...
...
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