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LieberInstitute / goesHyde_mdd_rnaseq

Fernando Goes and Thomas Hyde MDD RNA-seq project
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Compute weights row.names/colnames error #12

Closed aseyedia closed 3 years ago

aseyedia commented 3 years ago

The row names from the transformed expression file do not match up with the column names of the genotype file. This is throwing an error for the PredictDB-Tutorial weight computation script. 

> head(samples)
[1] "4572348328_R01C01" "4463344451_R01C01" "9829181016_R04C01"
[4] "9828658132_R03C01" "4256126291_A"      "4463344439_R01C02"

vs

> head(colnames(gt_df))
[1] "varID"    "R01C02"   "R01C02.1" "R01C01"   "R01C01.1" "R01C02.2"

As you can see, some function applied make.names to the column names of the genotype files. I need to find a way to get the column names from the genotype file and swap them with the full sample names from the rows of the expression file.

The script to worked on in question is https://github.com/LieberInstitute/goesHyde_mdd_rnaseq/blob/master/predixcan_pipeline/code/02_prep_inputs/02_process_snp_anno.R

aseyedia commented 3 years ago

I should have closed this issue a while ago