loadStudy error

[gadepallivs]

@LiNk-NY I have an issue when trying to load the data. The issue seems to be with the data_sv. txt/ Where we have multiple clumns Site_1_Chromosome, Site_2_Chromosome etc. Probably, not your package issue ?

exdir <- cBioPortalData::downloadStudy("coadread_tcga_pan_can_atlas_2018",
                                       use_cache = T,
                                       force = T)
file_dir <- cBioPortalData::untarStudy(exdir)
coadread <- cBioPortalData::loadStudy(file_dir)

Same error even if I use the new function

mae <- cBioPortalData::cBioDataPack("coadread_tcga_pan_can_atlas_2018")

Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
In addition: Warning messages:
1: Unable to import: mrna_seq_v2_rsem
Reason: missing value where TRUE/FALSE needed 
2: Unable to import: mrna_seq_v2_rsem_zscores_ref_all_samples
Reason: missing value where TRUE/FALSE needed 
3: Unable to import: mrna_seq_v2_rsem_zscores_ref_normal_samples
Reason: missing value where TRUE/FALSE needed 

[LiNk-NY]

Hi @gadepallivs

Thanks for the issue.
It looks like there is an issue with the data format:

Working on: /tmp/Rtmp3ycOFc/be6379645654_coadread_tcga_pan_can_atlas_2018/coadread_tcga_pan_can_atlas_2018/data_sv.txt
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names

You can report this to @cbioportal/cbioportal

Note. You can also try using readr::read_delim to read the file.

Best,
Marcel