I am a graduate student majoring in immunology. Recently, I've been working on single cell Sequence Data and trying to analyze BCR Sequence Data from 10x Chromium with the Package 'Platypus version 3.4.1'. I'm stuck on the first step using function VDJ_GEX_matrix. I copied and pasted the function wrote in vignettes as follows:
VDJ.out.directory.list[[1]] <- c("./BCR Data/VDJ5/")
GEX.out.directory.list <- list()
GEX.out.directory.list[[1]] <- c("./BCR Data/GEX5/")
vgm <- VDJ_GEX_matrix(VDJ.out.directory.list = VDJ.out.directory.list, GEX.out.directory.list = GEX.out.directory.list,GEX.integrate = T, VDJ.combine = T, integrate.GEX.to.VDJ = T, integrate.VDJ.to.GEX = T)
(VDJ5 and GEX5 are the direct output folder of CellRanger)
it resulted in an error like this:
Error in VDJ.proc$Nr_of_VJ_chains == 0 && VDJ.proc$Nr_of_VDJ_chains == :
'length = 78' in coercion to 'logical(1)'
First I thought that there might be some problems in my files, so I tried same process with the example files given by the Platypus, but the result was same. Maybe some structures or syntax in the function VDJ_GEX_matrix() is wrong or maybe other problems I cannot catch.
How should I deal with this problem?
p.s. Is there any recommended packages for analyzing BCR Repertoires? (eg. clonotypes, somatic hyper-mutation rate, etc.)