Reading in bead studio results not from Neogen

[khuhu]

Hi,

I got back my data from a genomics core where I used GIGA-MUGA to sequence 48 samples on half a panel. I tried to use the read.beadstudio function after loading in the SNP table; however, I get error below. Looks like it's expecting a Final_Report file containing the additional columns like X, Y Allele 1 ... etc. I do have these data but they're in individualized Final Reports. The only Final Report file containing all 48 samples is a matrix of genotypes where the rows and columns are SNP IDs and sample respectively. After reading the vignette I assume Neogen provides a concatenated version of the Final Reports file that your function expects? Is there an another way to read in the individualized final reports and concatenate them afterwards? Alternatively, it may be easier if you could provide an example of the concatenated Final Reports file Neogen gives you. I could try to create the concatenated file myself to fit the read.beadstudio function. Much appreciated.

> read.beadstudio(prefix = "Prjt_399_Udager_20220322_5516-KH_ffpe",
+                 in.path = "/br_z1/kevin_storage/advancedGenomicsCore/5516-KH/Prjt_399_Udager_20220318_5516-KH/Reports/",
+                 snps = snps)
Reading sample manifest from < /br_z1/kevin_storage/advancedGenomicsCore/5516-KH/Prjt_399_Udager_20220318_5516-KH/Reports//Sample_Map.txt > ...
Reading genotypes and intensities for 143446 markers x 48 samples from < /br_z1/kevin_storage/advancedGenomicsCore/5516-KH/Prjt_399_Udager_20220318_5516-KH/Reports//Prjt_399_Udager_20220322_5516-KH_ffpe_FinalReport.txt > ...
Error in .read.illumina.raw(prefix, in.path, colmap, check.dims = verify) : 
  All of the required column names were not found in the FinalReport file. The missing column(s) are: SNP Name, Sample ID, X, Y, Allele1 - Forward, Allele2 - Forward

[khuhu]

Figured out expected Neogen FinalReport1.txt by looking at another issue.