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MeRIPSeq
Commits
dbc973de
Commit
dbc973de
authored
6 years ago
by
Christophe BECAVIN
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add Guitar
parent
28481998
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2 changed files
src/R/diff_methyl.R
+16
-4
16 additions, 4 deletions
src/R/diff_methyl.R
src/R/guitar_plot.R
+4
-4
4 additions, 4 deletions
src/R/guitar_plot.R
with
20 additions
and
8 deletions
src/R/diff_methyl.R
+
16
−
4
View file @
dbc973de
...
...
@@ -11,11 +11,23 @@ rm(list=ls()) # remove all the objects from the R session
general_path
<-
"/Users/cbecavin/Documents/m6aAkker/"
#general_path <- "/pasteur/projets/policy01/m6aAkker/"
project_name
<-
"LivOld"
peak_name
<-
"LivOld"
# expr1 = read.delim(file="GSM462282_exp.txt")
# expr2 = read.delim(file="GSM462283_exp.txt")
# expr3 = read.delim(file="GSM462284_exp.txt")
# expr<- merge(expr1,expr2,by = "ID",all = TRUE)
# expr<- merge(expr,expr3,by = "ID",all = TRUE)
# expr$'Am_vs_GF' = expr$Am - expr$GF
# expr$'Plant_vs_GF' = expr$Plant - expr$GF
# expr$'Plant_vs_Am' = expr$Plant - expr$Am
# affy_probe = read.delim(file="Affy_probes.txt")
# final <- merge(expr,affy_probe, by.all="ID", all = TRUE)
# write.table(final,file="GEO_diff_exp_annot.txt",sep="\t",quote=FALSE,row.names = FALSE)
project_name
<-
"CecAm"
peak_name
<-
"CecAm"
project_dir
<-
paste
(
general_path
,
"PeakDiffExpression/"
,
project_name
,
"/"
,
sep
=
""
)
annotation_name
<-
"gencode.vM13"
exp_design_name
<-
"
LivOld
"
exp_design_name
<-
"
CecAm
"
exp_design_file
=
paste
(
project_dir
,
"/../../ExpDesign/"
,
exp_design_name
,
"_exp_design.txt"
,
sep
=
""
)
#rscript_folder <- "/pasteur/projets/policy01/m6aAkker/MeRIPSeq/src/R/"
...
...
@@ -78,7 +90,7 @@ save_contrast()
diff_summary
()
# # Do GUITAR plot (long execution time)
#
guitar_plot()
guitar_plot
()
# Plot PCA and Heatmap of differentially methylated sites
filter_table
<-
data.frame
(
norm_voom_epi
[
diff_peaks
,])
...
...
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src/R/guitar_plot.R
+
4
−
4
View file @
dbc973de
...
...
@@ -5,13 +5,13 @@ guitar_plot <- function(){
# Init Guitar plot
print
(
"Init GUITAR plot"
)
guitar_file
<-
paste
(
"../../temp/"
,
annotation_name
,
"_guitar.RData"
,
sep
=
""
)
if
(
!
file.exists
(
guitar_file
)){
#
if(!file.exists(guitar_file)){
gencodeVM13
<-
makeTxDbFromGFF
(
paste
(
"../../Genome/"
,
annotation_name
,
".annotation.gtf"
,
sep
=
""
),
format
=
"gtf"
)
gc_mm10_txdb
<-
makeGuitarCoordsFromTxDb
(
gencodeVM13
)
save
(
gc_mm10_txdb
,
file
=
guitar_file
)
}
else
{
load
(
guitar_file
)
}
#
}else{
#
load(guitar_file)
#
}
# Set data for Guitar plot
list_name
<-
list
(
""
,
"_Meth"
,
"_Meth_Epi"
,
"_MethGene"
,
"_MethNoGene"
)
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