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BDS
GeneDER
GeneDER_core
Commits
a42c7580
Commit
a42c7580
authored
Nov 11, 2020
by
Leon-Charles Tranchevent
Browse files
Refactoring step 04 to process all datasets at once (Second part - after match).
parent
f2e78969
Changes
6
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04-Prepare_datasets/Makefile
View file @
a42c7580
...
...
@@ -15,7 +15,5 @@ ps:
@
sbatch
${CODE_FOLDER}
create_probelists.sh
match
:
@
sbatch
${CODE_FOLDER}
match_probes.sh
biomarker
:
@
sbatch
${CODE_FOLDER}
plot_biomarkers.sh
doc
:
@
sbatch
${CODE_FOLDER}
doc.sh
@
sbatch
${CODE_FOLDER}
doc.sh
\ No newline at end of file
04-Prepare_datasets/doc.sh
View file @
a42c7580
...
...
@@ -122,29 +122,11 @@ do
echo
' }'
>>
${
OUTPUT_FOLDER
}
results_summary.tex
echo
'\end{figure}'
>>
${
OUTPUT_FOLDER
}
results_summary.tex
echo
''
>>
${
OUTPUT_FOLDER
}
results_summary.tex
done
echo
'\clearpage'
>>
${
OUTPUT_FOLDER
}
results_summary.tex
echo
''
>>
${
OUTPUT_FOLDER
}
results_summary.tex
# Per biomarker analysis.
nbBiomarkers
=
${#
biomarkers__name
[@]
}
for
((
i
=
0
;
i<
$nbBiomarkers
;
i++
))
do
biomarkerName
=
${
biomarkers__name
[
$i
]
}
biomarkerTissue
=
${
biomarkers__tissue
[
$i
]
}
biomarkerTissueForFile
=
${
biomarkerTissue
/ /_
}
echo
'\begin{figure}[ht]'
>>
${
OUTPUT_FOLDER
}
results_summary.tex
echo
' \centering'
>>
${
OUTPUT_FOLDER
}
results_summary.tex
echo
' \includegraphics[scale=0.43]{'
"
$OUTPUT_FOLDER
"
'Biomarker_'
"
${
biomarkerTissueForFile
}
"
'_'
"
${
biomarkerName
}
"
'.png}'
>>
${
OUTPUT_FOLDER
}
results_summary.tex
echo
' \caption{Expression values for biomarker '
"
${
biomarkerName
}
"
' for both DA and SN tissues.'
>>
${
OUTPUT_FOLDER
}
results_summary.tex
echo
' (Top) Usage of expression values as derived from pre-processing. (Bottom) Usage of Z-scores '
>>
${
OUTPUT_FOLDER
}
results_summary.tex
echo
' derived from the expression values. (Left) VSN correction applied. (Right) No VSN correction applied.}'
>>
${
OUTPUT_FOLDER
}
results_summary.tex
echo
'\end{figure}'
>>
${
OUTPUT_FOLDER
}
results_summary.tex
echo
'\clearpage'
>>
${
OUTPUT_FOLDER
}
results_summary.tex
echo
''
>>
${
OUTPUT_FOLDER
}
results_summary.tex
done
done
# Print footer
echo
''
>>
${
OUTPUT_FOLDER
}
results_summary.tex
...
...
04-Prepare_datasets/match_probes.R
View file @
a42c7580
...
...
@@ -377,7 +377,8 @@ for (i in seq_len(length(config$platforms))) {
dplyr
::
rename
(
!!
platform
$
platform_name
:=
probesets
)
rm
(
deps_matching
,
matching_dataset
,
platform
)
}
# End for each platform.
rm
(
i
,
genes_probe_matching
,
geneset_probe_matching
)
#rm(i, genes_probe_matching, geneset_probe_matching)
rm
(
i
)
# We merge the dataframes, create one global matching dataframe and save it.
global_matching_data_merged
<-
NULL
...
...
0
4-Prepare_dataset
s/plot_biomarkers.R
→
0
5-Get_DEG
s/plot_biomarkers.R
View file @
a42c7580
File moved
0
4-Prepare_dataset
s/plot_biomarkers.sh
→
0
5-Get_DEG
s/plot_biomarkers.sh
View file @
a42c7580
File moved
0
4-Prepare_dataset
s/plot_biomarkers_withdiseasestatus.R
→
0
5-Get_DEG
s/plot_biomarkers_withdiseasestatus.R
View file @
a42c7580
File moved
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