Commit 9bcf8e0b authored by Christian Mertes's avatar Christian Mertes
parents 9be7be12 9956e174
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This code repository is linked to the publication of
This code repository is associated to the publication of
<a href="http://biorxiv.org/content/early/2016/07/29/066738)">Kremer, Bader et al. (2016 bioRxiv)</a>.
Source code of the main processing steps and to reproduce the figures of the paper is provided here.
......@@ -6,10 +6,14 @@ Source code of the main processing steps and to reproduce the figures of the pap
1. Download our figures, supplemental and extended supplemental data here:
http://i12g-gagneurweb.in.tum.de/public/paper/mitoMultiOmics/.
You need the figures, since some panles are manually created and cannot be reproduced entirely with data and R code, i.e. pedigree or IGV pictures.
You need the figures, since some panels are manually created and cannot be reproduced entirely with data and R code, i.e. pedigree or IGV pictures.
2. Adjust these two parameters PAPERSHAREDIR and FIGDIR in "paper_config_params.R" to point to your downloads
2. Adjust these two parameters PAPERSHAREDIR and FIGDIR in
<a herf="https://i12g-gagneurweb.informatik.tu-muenchen.de/gitlab/baderda/mitoMultiOmics_public/blob/master/paper_natgen/paper_config_params.R">
paper_config_params.R</a> to point to your downloads
3. Source any of the fig*.R scripts. Note the packages required to plot are listed in "paper_config_packages.R"
3. Source any of the fig*.R scripts to re-plot any paper figure. Note: the packages required are listed in
<a href="https://i12g-gagneurweb.informatik.tu-muenchen.de/gitlab/baderda/mitoMultiOmics_public/blob/master/paper_natgen/paper_config_packages.R">
paper_config_packages.R</a>
Enjoy plotting!
paper_create_rawdata.R
paper_create_rawdata.html
......@@ -20,9 +20,6 @@ EXID = "65990"
# variants per sample
mae_variant_counts_list = readRDS(FILE_mono_allelic_expression)
# mae deseq result
dds_mae <- readRDS( get_paper_file_mae_deseq(FIB) )
# metabolite intensities
metabolome = read.delim(FILE_metabolome, check.names=F)
......
......@@ -6,11 +6,15 @@
<body>
<h1>Index of /public/paper/mitoMultiOmics</h1>
<p>
This folder contains the extended supplementary data for Kremer and Bader et al. 2016 biorXiv<br>
* The paper can be found <a href="http://biorxiv.org/content/early/2016/07/29/066738" >here</a><br>
* The source code to reproduce the figures can be found <a href="gitlab/mitoMultiOmics_public/" >here</a>
This folder contains the extended supplementary data for Kremer and Bader et al. 2016 biorXiv
<br>
* The paper can be found
<a href="http://biorxiv.org/content/early/2016/07/29/066738" >here</a>
<br>
* The source code to reproduce the figures can be found
<a href="http://i12g-gagneurweb.informatik.tu-muenchen.de/gitlab/baderda/mitoMultiOmics_public/" >here</a>
<br>
<br>
To download all files type: wget -rc http://i12g-gagneurweb.in.tum.de/public/paper/mitoMultiOmics
</p>
</html>
......@@ -6,16 +6,8 @@
get_mae_results_for_ma_plot = function(fibroid, filter_coverage= 10){
# get large DESeq fit and results
dds_mae <- readRDS( get_paper_file_mae_deseq(FIB) )
res_dds_mae = fread(get_paper_file_mae_deseq(FIB) )
# basic data.table
res_dds_mae = data.table(
hgncid = rownames(dds_mae$res),
padj = dds_mae$res$padj,
exacmaf= mcols(dds_mae$dds)[,'exacmaf'],
alt_allele_freq= mcols(dds_mae$dds)[,'alt_allele_freq'],
coverage= mcols(dds_mae$dds)[,'coverage']
)
# coverage filter
res_dds_mae = res_dds_mae[coverage > filter_coverage]
......
......@@ -16,7 +16,7 @@ tmpnull= sapply(list.files(file.path("src/r/paper_natgen/functions"), full.names
# get patient specific ect suppl files
get_paper_file_mae_deseq = function(fibroid){
paste0(extsuppl_prefix, fibroid, '_mae_deseq_results.RDS')
paste0(extsuppl_prefix, fibroid, '_mae_deseq_results.tsv')
}
get_paper_file_patient_report = function(fibroid){
......
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