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MeRIPSeq
Commits
fbe7f857
Commit
fbe7f857
authored
6 years ago
by
Christophe BECAVIN
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Update diff_meth.R by removing RNA_IP management
parent
9e26d933
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4 changed files
INSTALL.txt
+1
-3
1 addition, 3 deletions
INSTALL.txt
src/bash_slurm/RunDiffMeth.sh
+2
-2
2 additions, 2 deletions
src/bash_slurm/RunDiffMeth.sh
src/diff_methyl.R
+7
-3
7 additions, 3 deletions
src/diff_methyl.R
src/m6aAnalysis/R/plot_description.R
+12
-12
12 additions, 12 deletions
src/m6aAnalysis/R/plot_description.R
with
22 additions
and
20 deletions
INSTALL.txt
+
1
−
3
View file @
fbe7f857
...
...
@@ -76,11 +76,9 @@ conda install bioconductor-biomart
conda install bioconductor-edger
conda install bioconductor-genomicfeatures
conda install r-sartools
conda install bioconductor-sva
# in R
install.packages(c("ggplot2","gplots","ggfortify","RColorBrewer","seqinr","dendextend"))
install.packages(c("pheatmap","GGally"))
This diff is collapsed.
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src/bash_slurm/RunDiffMeth.sh
+
2
−
2
View file @
fbe7f857
...
...
@@ -19,8 +19,8 @@ file_name=${exp_design_name}_${bed_name}
if
[
!
-d
$folder
/temp/
${
SLURM_JOB_NAME
}
]
;
then
mkdir
$folder
/temp/
${
SLURM_JOB_NAME
}
fi
shFile
=
/pasteur/projets/policy01/m6aAkker/temp/
${
SLURM_JOB_NAME
}
/
${
file_name
}
_
${
SLURM_JOB_NAME
}
.sh
logFile
=
/pasteur/projets/policy01/m6aAkker/temp/
${
SLURM_JOB_NAME
}
/
${
file_name
}
_
${
SLURM_JOB_NAME
}
.log
shFile
=
/pasteur/projets/policy01/m6aAkker/temp/
${
SLURM_JOB_NAME
}
/
${
file_name
}
_
${
SLURM_JOB_NAME
}
_
${
SLURM_JOB_ID
}
.sh
logFile
=
/pasteur/projets/policy01/m6aAkker/temp/
${
SLURM_JOB_NAME
}
/
${
file_name
}
_
${
SLURM_JOB_NAME
}
_
${
SLURM_JOB_ID
}
.log
# Create script SH to run in qsub
scriptSH
=
"""
...
...
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src/diff_methyl.R
+
7
−
3
View file @
fbe7f857
...
...
@@ -59,6 +59,8 @@ if(file.exists(rdata_file)){
color_biocond
<-
c
(
"seagreen4"
,
"seagreen3"
,
"gray0"
,
"gray51"
,
"tan4"
,
"tan3"
,
"firebrick1"
)
}
else
if
(
exp_design_name
==
"LivOld"
){
color_biocond
<-
c
(
"seagreen4"
,
"gray0"
,
"dodgerblue"
,
"tan4"
)
}
else
{
color_biocond
<-
c
(
"seagreen4"
,
"seagreen3"
,
"gray0"
,
"gray51"
,
"tan4"
,
"tan3"
,
"firebrick1"
)
}
init_parameters
()
...
...
@@ -103,9 +105,9 @@ if(file.exists(rdata_file)){
filter_table
<-
data.frame
(
norm_voom_epi
[
diff_peaks
,])
plot_heatmap
(
filter_table
,
""
)
plot_pca
(
filter_table
,
""
)
filter_table
<-
filter_table
[,
colnames
(
filter_table
)
%in%
colnames
(
counts_RNA_IP
)]
plot_heatmap
(
filter_table
,
"_IP"
)
plot_pca
(
filter_table
,
"_IP"
)
#
filter_table <- filter_table[,colnames(filter_table) %in% colnames(counts_RNA_IP)]
#
plot_heatmap(filter_table,"_IP")
#
plot_pca(filter_table,"_IP")
filter_table
<-
data.frame
(
norm_voom_epi
[
diff_peaks
,])
filter_table
<-
filter_table
[,
colnames
(
filter_table
)
%in%
colnames
(
counts_RNA_I
)]
plot_heatmap
(
filter_table
,
"_Input"
)
...
...
@@ -114,6 +116,8 @@ if(file.exists(rdata_file)){
plot_heatmap
(
filter_table
,
"_Gene"
)
plot_pca
(
filter_table
,
"_Gene"
)
print
(
"Save RData"
)
print
(
rdata_file
)
save.image
(
rdata_file
)
}
...
...
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src/m6aAnalysis/R/plot_description.R
+
12
−
12
View file @
fbe7f857
...
...
@@ -23,18 +23,18 @@ plot_description <- function(){
}
write.table
(
counts_RNA_I
[
order
(
counts_RNA_I
[,
1
],
decreasing
=
TRUE
)[
1
:
50
],],
file
=
paste
(
image_folder
,
peak_name
,
"_Count_RNA_Input.xls"
,
sep
=
""
),
quote
=
FALSE
,
row.names
=
FALSE
,
sep
=
"\t"
)
majSequences
<-
descriptionPlots
(
counts
=
counts_RNA_IP
,
group
=
target_RNA_IP
[,
varInt
],
col
=
color_biocond
)
image_folder
=
paste
(
project_dir
,
"FiguresRNAIP/"
,
sep
=
""
)
if
(
!
dir.exists
(
image_folder
)){
file.rename
(
from
=
"figures/"
,
to
=
image_folder
)
}
else
{
unlink
(
image_folder
,
recursive
=
TRUE
)
file.rename
(
from
=
"figures/"
,
to
=
image_folder
)
}
write.table
(
counts_RNA_IP
[
order
(
counts_RNA_IP
[,
1
],
decreasing
=
TRUE
)[
1
:
50
],],
file
=
paste
(
image_folder
,
peak_name
,
"_Count_RNA_IP.xls"
,
sep
=
""
),
quote
=
FALSE
,
row.names
=
FALSE
,
sep
=
"\t"
)
if
(
!
dir.exists
(
figure_folder
)){
dir.create
(
figure_folder
)
}
#
majSequences <- descriptionPlots(counts=counts_RNA_IP, group=target_RNA_IP[,varInt], col=color_biocond)
#
image_folder = paste(project_dir,"FiguresRNAIP/",sep="")
#
if (!dir.exists(image_folder)){
#
file.rename(from="figures/",to=image_folder)
#
}else{
#
unlink(image_folder, recursive=TRUE)
#
file.rename(from="figures/",to=image_folder)
#
}
#
write.table( counts_RNA_IP[order(counts_RNA_IP[,1],decreasing = TRUE)[1:50],], file=paste(image_folder, peak_name,"_Count_RNA_IP.xls",sep=""), quote=FALSE, row.names = FALSE, sep = "\t")
#
if (!dir.exists(figure_folder)){
#
dir.create(figure_folder)
#
}
# majSequences <- descriptionPlots(counts=counts_Trans_I, group=target_RNA_I[,varInt], col=color_biocond)
# image_folder = paste(project_dir,"FiguresTranscrI/",sep="")
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