Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Sign in / Register
Toggle navigation
Menu
Open sidebar
Strand Lab
sc-TissueMapper
Commits
23afe24b
Commit
23afe24b
authored
May 06, 2019
by
Gervaise Henry
🤠
Browse files
Update QuSAGE including leu ID with cybersort
parent
b5f7d29a
Changes
1
Hide whitespace changes
Inline
Side-by-side
r.scripts/QuSAGE.R
View file @
23afe24b
source
(
"./r.scripts/sc-TissueMapper_functions.R"
)
source
(
"./r.scripts/sc-TissueMapper_process.R"
)
# gene.set1 <- read_delim("./genesets/DEG_Epi_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
# gene.set1 <- as.list(gene.set1)
...
...
@@ -91,10 +93,27 @@ names(gene.set.leu.lin)[1:12] <- "Lymphoid"
names
(
gene.set.leu.lin
)[
13
:
22
]
<-
"Myeloid"
gene.set.lym
<-
gene.set
[
9
:
20
]
# names(gene.set.lym)[1:2] <- "B cells"
# names(gene.set.lym)[3] <- "Plasma cells"
# names(gene.set.lym)[3] <- "CD8 T cells"
# names(gene.set.lym)[5:9] <- "CD4 T cells"
# names(gene.set.lym)[10] <- "Gamma delta T cells"
gene.set.myl
<-
gene.set
[
21
:
30
]
# names(gene.set.lym)[1:4] <- "Monocytes and Macrophages"
# names(gene.set.lym)[5:6] <- "Dendritic cells"
# names(gene.set.lym)[7:8] <- "Mast cells"
# names(gene.set.lym)[9] <- "Eosinophil"
# names(gene.set.lym)[10] <- "Neutrophil"
rm
(
gene.set1
)
results
<-
scQuSAGE
(
sc10x
,
gs
=
gene.set
,
save
=
TRUE
,
type
=
"lg"
,
id
=
"integrated_snn_res.5"
,
ds
=
0
,
nm
=
"ALL"
,
print
=
"2"
)
sc10x
<-
results
[[
1
]]
results.cor.lin
<-
results
[[
2
]]
results.clust.lin.id
<-
results
[[
3
]]
rm
(
results
)
results
<-
scQuSAGE
(
sc10x
,
gs
=
gene.set.lin
,
save
=
TRUE
,
type
=
"lg"
,
id
=
"integrated_snn_res.0.1"
,
ds
=
0
,
nm
=
"lin"
,
print
=
"2"
)
sc10x
<-
results
[[
1
]]
results.cor.lin
<-
results
[[
2
]]
...
...
@@ -105,26 +124,25 @@ sc10x.epi <- scSubset(sc10x,i="lin","Epi")
sc10x.st
<-
scSubset
(
sc10x
,
i
=
"lin"
,
"St"
)
sc10x.leu
<-
scSubset
(
sc10x
,
i
=
"lin"
,
"Leu"
)
results
<-
scPC
(
sc10x.epi
,
pc
=
5
0
,
hpc
=
0.9
,
file
=
"epi"
,
print
=
"2"
,
cca
=
TRUE
)
results
<-
scPC
(
sc10x.epi
,
pc
=
10
0
,
hpc
=
0.9
,
file
=
"epi"
,
print
=
"2"
)
sc10x.epi
<-
results
[[
1
]]
pc.use.epi
<-
results
[[
2
]]
rm
(
results
)
sc10x.epi
<-
scCluster
(
sc10x.epi
,
res
=
res
,
red
=
"pca"
,
dim
=
pc.use.epi
,
print
=
"2"
,
folder
=
"epi"
)
results
<-
scPC
(
sc10x.st
,
pc
=
5
0
,
hpc
=
0.9
,
file
=
"st"
,
print
=
"2"
,
cca
=
TRUE
)
results
<-
scPC
(
sc10x.st
,
pc
=
10
0
,
hpc
=
0.9
,
file
=
"st"
,
print
=
"2"
)
sc10x.st
<-
results
[[
1
]]
pc.use.st
<-
results
[[
2
]]
rm
(
results
)
sc10x.st
<-
scCluster
(
sc10x.st
,
res
=
res
,
red
=
"pca"
,
dim
=
pc.use.st
,
print
=
"2"
,
folder
=
"st"
)
results
<-
scPC
(
sc10x.leu
,
pc
=
5
0
,
hpc
=
0.9
,
file
=
"leu"
,
print
=
"2"
,
cca
=
TRUE
)
results
<-
scPC
(
sc10x.leu
,
pc
=
10
0
,
hpc
=
0.9
,
file
=
"leu"
,
print
=
"2"
)
sc10x.leu
<-
results
[[
1
]]
pc.use.leu
<-
results
[[
2
]]
rm
(
results
)
sc10x.leu
<-
scCluster
(
sc10x.leu
,
res
=
res
,
red
=
"pca"
,
dim
=
pc.use.leu
,
print
=
"2"
,
folder
=
"leu.lin"
)
#min <- min(table(sc10x$integrated_snn_res.1))
results
<-
scQuSAGE
(
sc10x.epi
,
gs
=
gene.set.epi
,
save
=
TRUE
,
type
=
"lg"
,
id
=
"integrated_snn_res.1"
,
ds
=
0
,
nm
=
"epi"
,
print
=
"2"
)
results
<-
scQuSAGE
(
sc10x.epi
,
gs
=
gene.set.epi
,
save
=
TRUE
,
type
=
"lg"
,
id
=
"integrated_snn_res.0.5"
,
ds
=
0
,
nm
=
"epi"
,
print
=
"2"
)
sc10x.epi
<-
results
[[
1
]]
results.cor.epi
<-
results
[[
2
]]
results.clust.epi.id
<-
results
[[
3
]]
...
...
@@ -136,7 +154,7 @@ results.cor.st <- results[[2]]
results.clust.st.id
<-
results
[[
3
]]
rm
(
results
)
results
<-
scQuSAGE
(
sc10x.leu
,
gs
=
gene.set.leu.lin
,
save
=
TRUE
,
type
=
"lg"
,
id
=
"integrated_snn_res.0.
2
"
,
ds
=
0
,
nm
=
"leu.lin"
,
print
=
"2"
)
results
<-
scQuSAGE
(
sc10x.leu
,
gs
=
gene.set.leu.lin
,
save
=
TRUE
,
type
=
"lg"
,
id
=
"integrated_snn_res.0.
5
"
,
ds
=
0
,
nm
=
"leu.lin"
,
print
=
"2"
)
sc10x.leu.lin
<-
results
[[
1
]]
results.cor.leu.lin
<-
results
[[
2
]]
results.clust.leu.lin.id
<-
results
[[
3
]]
...
...
@@ -145,25 +163,25 @@ rm(results)
sc10x.lym
<-
scSubset
(
sc10x.leu.lin
,
i
=
"leu.lin"
,
"Lymphoid"
)
sc10x.myl
<-
scSubset
(
sc10x.leu.lin
,
i
=
"leu.lin"
,
"Myeloid"
)
results
<-
scPC
(
sc10x.lym
,
pc
=
5
0
,
hpc
=
0.9
,
file
=
"lym"
,
print
=
"2"
,
cca
=
TRUE
)
results
<-
scPC
(
sc10x.lym
,
pc
=
10
0
,
hpc
=
0.9
,
file
=
"lym"
,
print
=
"2"
)
sc10x.lym
<-
results
[[
1
]]
pc.use.lym
<-
results
[[
2
]]
rm
(
results
)
sc10x.lym
<-
scCluster
(
sc10x.lym
,
res
=
res
,
red
=
"pca"
,
dim
=
pc.use.lym
,
print
=
"2"
,
folder
=
"lym"
)
results
<-
scPC
(
sc10x.myl
,
pc
=
5
0
,
hpc
=
0.9
,
file
=
"myl"
,
print
=
"2"
,
cca
=
TRUE
)
results
<-
scPC
(
sc10x.myl
,
pc
=
10
0
,
hpc
=
0.9
,
file
=
"myl"
,
print
=
"2"
)
sc10x.myl
<-
results
[[
1
]]
pc.use.myl
<-
results
[[
2
]]
rm
(
results
)
sc10x.myl
<-
scCluster
(
sc10x.myl
,
res
=
res
,
red
=
"pca"
,
dim
=
pc.use.myl
,
print
=
"2"
,
folder
=
"myl"
)
results
<-
scQuSAGE
(
sc10x.lym
,
gs
=
gene.set.lym
,
save
=
TRUE
,
type
=
"lg"
,
id
=
"integrated_snn_res.
0.5
"
,
ds
=
0
,
nm
=
"lym"
,
print
=
"2"
)
results
<-
scQuSAGE
(
sc10x.lym
,
gs
=
gene.set.lym
,
save
=
TRUE
,
type
=
"lg"
,
id
=
"integrated_snn_res.
1
"
,
ds
=
0
,
nm
=
"lym"
,
print
=
"2"
)
sc10x.lym
<-
results
[[
1
]]
results.cor.lym
<-
results
[[
2
]]
results.clust.lym.id
<-
results
[[
3
]]
rm
(
results
)
results
<-
scQuSAGE
(
sc10x.myl
,
gs
=
gene.set.myl
,
save
=
TRUE
,
type
=
"
lg
"
,
id
=
"integrated_snn_res.
0.5
"
,
ds
=
0
,
nm
=
"myl"
,
print
=
"2"
)
results
<-
scQuSAGE
(
sc10x.myl
,
gs
=
gene.set.myl
,
save
=
TRUE
,
type
=
"
sm
"
,
id
=
"integrated_snn_res.
1
"
,
ds
=
0
,
nm
=
"myl"
,
print
=
"2"
)
sc10x.myl
<-
results
[[
1
]]
results.cor.myl
<-
results
[[
2
]]
results.clust.myl.id
<-
results
[[
3
]]
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment