Currently the get_gene_expression function only works for users with morinlab group permissions because the config accesses only icgc_dart outputs. I've now updated my salmon/DESeq2 Snakefile to also generate the tidy gene expression matrix for each unix_group. Could you please update the function to use either the gambl version or icgc_dart version depending on a user's permission levels?
For those with morinlab permissions the file will be results/icgc_dart/DESeq2-0.0_salmon-1.0/mrna--gambl-icgc-all/vst-matrix-Hugo_Symbol_tidy.tsv (i.e. current status quo)
For those with only gambl permissions the file will be results/gambl/DESeq2-0.0_salmon-1.0/mrna/vst-matrix-Hugo_Symbol_tidy.tsv
Also, now that the Salmon Snakefile has been set up to generate the tidy matrix, we should consider modifying the current tidy_gene_expression function to NOT write to file by default as this will create some conflicts with the Snakefile version.
mattssca
commented
1 year ago
Currently the
get_gene_expressionfunction only works for users withmorinlabgroup permissions because the config accesses onlyicgc_dartoutputs. I've now updated my salmon/DESeq2 Snakefile to also generate the tidy gene expression matrix for each unix_group. Could you please update the function to use either thegamblversion oricgc_dartversion depending on a user's permission levels?For those with
morinlabpermissions the file will beresults/icgc_dart/DESeq2-0.0_salmon-1.0/mrna--gambl-icgc-all/vst-matrix-Hugo_Symbol_tidy.tsv(i.e. current status quo)For those with only
gamblpermissions the file will beresults/gambl/DESeq2-0.0_salmon-1.0/mrna/vst-matrix-Hugo_Symbol_tidy.tsvAlso, now that the Salmon Snakefile has been set up to generate the tidy matrix, we should consider modifying the current
tidy_gene_expressionfunction to NOT write to file by default as this will create some conflicts with the Snakefile version.