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petsalakilab
2D_CRISPR_LibraryGeneSelection
Commits
9a61c991
Commit
9a61c991
authored
Sep 06, 2021
by
Sayed Rzgar Hosseini
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9a61c991
######################################################################################################################################################################################################
anchor_breast
<-
read.csv
(
"./Tables/Table10.csv"
)
$
Gene
anchor_colorectal
<-
read.csv
(
"./Tables/Table11.csv"
)
$
Gene
Candidate_Breast
<-
read.csv
(
"./Tables/Table8.csv"
)
$
x
Candidate_Colorectal
<-
read.csv
(
"./Tables/Table9.csv"
)
$
x
######################################################################################################################################################################################################
GlobalESS
<-
readRDS
(
"./SupplementaryData/SupplementaryData2/Global_ess_corr.rds"
)
Edges
<-
readRDS
(
"./SupplementaryData/SupplementaryData2/EDGES.rds"
)
######################################################################################################################################################################################################
#Breast
coessential_breast2
<-
list
()
all_coess_breast2
<-
c
()
for
(
i
in
1
:
40
){
print
(
i
)
set1
<-
which
(
Edges
$
from
==
as.character
(
anchor_breast
[
i
]))
set2
<-
which
(
Edges
$
dashes
==
FALSE
)
set3
<-
union
(
which
(
Edges
$
modified_effector
==
"Mutation"
),
which
(
Edges
$
modified_effector
==
"Expression"
))
set4
<-
union
(
which
(
Edges
$
comparision_in
==
"Breast Cancer"
),
which
(
Edges
$
comparision_in
==
"Breast"
))
set5
<-
intersect
(
which
(
Edges
$
Confidence
==
"Group A"
),
which
(
Edges
$
width
>
1
))
set6
<-
intersect
(
which
(
Edges
$
median_group
>
0.5
),
which
(
Edges
$
median_group
>
Edges
$
median_other
))
selected
<-
intersect
(
intersect
(
intersect
(
set1
,
set2
),
intersect
(
set3
,
set4
)),
intersect
(
set5
,
set6
))
coessential_breast2
[[
i
]]
<-
unique
(
Edges
$
to
[
selected
])
all_coess_breast2
<-
c
(
all_coess_breast2
,
coessential_breast2
[[
i
]])
}
all_coess_breast2
<-
unique
(
all_coess_breast2
)
all_coess_breast2
<-
intersect
(
Candidate_Breast
,
all_coess_breast2
)
#Colorectal
coessential_colorectal2
<-
list
()
all_coess_colorectal2
<-
c
()
for
(
i
in
1
:
43
){
print
(
i
)
set1
<-
which
(
Edges
$
from
==
as.character
(
anchor_colorectal
[
i
]))
set2
<-
which
(
Edges
$
dashes
==
FALSE
)
set3
<-
union
(
which
(
Edges
$
modified_effector
==
"Mutation"
),
which
(
Edges
$
modified_effector
==
"Expression"
))
set4
<-
union
(
which
(
Edges
$
comparision_in
==
"Colorectal Cancer"
),
which
(
Edges
$
comparision_in
==
"Colon/Rectum"
))
set5
<-
intersect
(
which
(
Edges
$
Confidence
==
"Group A"
),
which
(
Edges
$
width
>
1
))
set6
<-
intersect
(
which
(
Edges
$
median_group
>
0.5
),
which
(
Edges
$
median_group
>
Edges
$
median_other
))
selected
<-
intersect
(
intersect
(
intersect
(
set1
,
set2
),
intersect
(
set3
,
set4
)),
intersect
(
set5
,
set6
))
coessential_colorectal2
[[
i
]]
<-
unique
(
Edges
$
to
[
selected
])
all_coess_colorectal2
<-
c
(
all_coess_colorectal2
,
coessential_colorectal2
[[
i
]])
}
all_coess_colorectal2
<-
unique
(
all_coess_colorectal2
)
all_coess_colorectal2
<-
intersect
(
Colorectal_Genes
,
all_coess_colorectal2
)
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