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mmassaviol
WAWmassaviol
Commits
cf84f6d1
Commit
cf84f6d1
authored
Oct 08, 2021
by
khalid
Browse files
debug deseq2 R script
parent
709cc54b
Changes
2
Hide whitespace changes
Inline
Side-by-side
tools/deseq2/deseq2.script.R
View file @
cf84f6d1
...
...
@@ -2,11 +2,9 @@
#sink(log)
#sink(log, type="message")
library
(
DESeq2
)
library
(
edgeR
)
library
(
apeglm
)
library
(
BiocParallel
)
library
(
tximport
)
library
(
rhdf5
)
library
(
GenomicFeatures
)
library
(
ggplot2
)
...
...
@@ -137,41 +135,40 @@ pheatmap(assayNTD[select,], cluster_rows=FALSE, show_rownames=FALSE, cluster_col
#heatmap(cpmTop,main = "Heatmap",margins = c(10,1))
dev.off
()
speciesData
=
snakemake
@
config
[[
"biomaRtDataset"
]]
speciesData
=
snakemake
@
params
[[
"biomaRtDataset"
]]
print
(
speciesData
)
if
(
speciesData
!=
"None"
)
{
# Add annotation with biomaRt
library
(
biomaRt
)
mart
<-
useMart
(
biomart
=
"ENSEMBL_MART_ENSEMBL"
,
host
=
"ensembl.org"
)
if
(
speciesData
!=
"None"
)
{
#Add annotation with biomaRt
library
(
biomaRt
)
mart
<-
useMart
(
biomart
=
"ENSEMBL_MART_ENSEMBL"
,
host
=
"ensembl.org"
)
species_mart
<-
useMart
(
biomart
=
"ENSEMBL_MART_ENSEMBL"
,
host
=
"ensembl.org"
,
dataset
=
speciesData
)
#for the moment the top genes change to significant genes ?
#what if we have tarnscript ID instead of gene ID ?
ann
<-
getBM
(
filter
=
"ensembl_gene_id"
,
value
=
rownames
(
topGenes
),
attributes
=
c
(
"ensembl_gene_id"
,
"description"
,
"transcript_length"
),
mart
=
species_mart
)
go_ann
<-
getBM
(
filter
=
"ensembl_gene_id"
,
value
=
rownames
(
topGenes
),
attributes
=
c
(
"ensembl_gene_id"
,
"description"
,
"go_id"
,
"name_1006"
,
"namespace_1003"
),
mart
=
species_mart
)
write.table
(
go_ann
,
paste
(
snakemake
@
output
[[
"Top_genes"
]],
"_mqc.tsv"
,
sep
=
"\t"
)
#test for gene enrichment with gprofiler2
library
(
gprofiler2
)
#for the moment the top genes change to significant genes ?
organisme
=
gsub
(
"_gene_ensembl"
,
""
,
speciesData
)
gostres
<-
gost
(
query
=
rownames
(
topGenes
),
organism
=
organisme
,
ordered_query
=
FALSE
,
multi_query
=
FALSE
,
significant
=
FALSE
,
exclude_iea
=
FALSE
,
measure_underrepresentation
=
FALSE
,
evcodes
=
FALSE
,
user_threshold
=
0.05
,
correction_method
=
"g_SCS"
,
domain_scope
=
"annotated"
,
custom_bg
=
NULL
,
numeric_ns
=
""
,
sources
=
NULL
,
as_short_link
=
FALSE
)
png
(
filename
=
paste0
(
snakemake
@
config
[[
"results_dir"
]],
"/"
,
snakemake
@
config
[[
"<step_name>__deseq2_output_dir"
]],
"/gprofiler2_mqc.png"
),
height
=
800
,
width
=
800
)
gostplot
(
gostres
,
capped
=
TRUE
,
interactive
=
TRUE
)
dev.off
()
species_mart
<-
useMart
(
biomart
=
"ENSEMBL_MART_ENSEMBL"
,
host
=
"ensembl.org"
,
dataset
=
)
#for the moment the top genes change to significant genes ?
#what if we have tarnscript ID instead of gene ID ?
ann
<-
getBM
(
filter
=
"ensembl_gene_id"
,
value
=
rownames
(
topGenes
),
attributes
=
c
(
"ensembl_gene_id"
,
"description"
,
"transcript_length"
),
mart
=
species_mart
)
go_ann
<-
getBM
(
filter
=
"ensembl_gene_id"
,
value
=
rownames
(
topGenes
),
attributes
=
c
(
"ensembl_gene_id"
,
"description"
,
"go_id"
,
"name_1006"
,
"namespace_1003"
),
mart
=
species_mart
)
write.table
(
go_ann
,
paste
(
snakemake
@
output
[[
"Top_genes"
]],
"_mqc.tsv"
,
sep
=
"\t"
))
#test for gene enrichment with gprofiler2
library
(
gprofiler2
)
#for the moment the top genes change to significant genes ?
organisme
=
gsub
(
"_gene_ensembl"
,
""
,
speciesData
)
gostres
<-
gost
(
query
=
rownames
(
topGenes
),
organism
=
organisme
,
ordered_query
=
FALSE
,
multi_query
=
FALSE
,
significant
=
FALSE
,
exclude_iea
=
FALSE
,
measure_underrepresentation
=
FALSE
,
evcodes
=
FALSE
,
user_threshold
=
0.05
,
correction_method
=
"g_SCS"
,
domain_scope
=
"annotated"
,
custom_bg
=
NULL
,
numeric_ns
=
""
,
sources
=
NULL
,
as_short_link
=
FALSE
)
png
(
filename
=
paste0
(
snakemake
@
config
[[
"results_dir"
]],
"/"
,
snakemake
@
config
[[
"<step_name>__deseq2_output_dir"
]],
"/gprofiler2_mqc.png"
),
height
=
800
,
width
=
800
)
gostplot
(
gostres
,
capped
=
TRUE
,
interactive
=
TRUE
)
dev.off
()
write.table
(
gostres
$
result
,
paste0
(
snakemake
@
config
[[
"results_dir"
]],
"/"
,
snakemake
@
config
[[
"<step_name>__deseq2_output_dir"
]],
"/gprofiler2_mqc.tsv"
),
sep
=
"\t"
)
write.table
(
gostres
$
result
,
paste0
(
snakemake
@
config
[[
"results_dir"
]],
"/"
,
snakemake
@
config
[[
"<step_name>__deseq2_output_dir"
]],
"/gprofiler2_mqc.tsv"
),
sep
=
"\t"
)
}
#cpmTop = cpm_counts[rownames(resSigdf),]
...
...
tools/deseq2/deseq2.yaml
View file @
cf84f6d1
...
...
@@ -59,7 +59,7 @@
type
:
select
,
choices
:
[
None
:
"
None"
,
Mus musculus
:
"
mm_gene_ensembl"
,
Mus musculus
:
"
mm
usculus
_gene_ensembl"
,
Homo sapiens
:
"
hsapiens_gene_ensembl"
,
Nile tilapia
:
"
oniloticus_gene_ensembl"
,
oniloticus_gene_ensembl
:
"
dmelanogaster_gene_ensembl"
...
...
@@ -92,7 +92,8 @@
tximport
:
[
'
Rscript
-e
'
'
BiocManager::install("tximport",
version
=
"3.10",Ncpus=8,
clean=TRUE);library("tximport")'
'
'
],
rhdf5
:
[
'
Rscript
-e
'
'
BiocManager::install("rhdf5",
version
=
"3.10",Ncpus=8,
clean=TRUE);library("rhdf5")'
'
'
],
GenomicFeatures
:
[
'
Rscript
-e
'
'
BiocManager::install("GenomicFeatures",
version
=
"3.10",Ncpus=8,
clean=TRUE);library("GenomicFeatures")'
'
'
],
pheatmap
:
[
'
Rscript
-e
'
'
install.packages("pheatmap",Ncpus=8,
clean=TRUE);library("pheatmap")'
'
'
]
pheatmap
:
[
'
Rscript
-e
'
'
install.packages("pheatmap",Ncpus=8,
clean=TRUE);library("pheatmap")'
'
'
],
certificates
:
[
apt-get install -y ca-certificates
]
},
script
:
deseq2.script.R
,
citations
:
{
...
...
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