Hi All,


I appreciate if anyone can provide an example to use DeepSNV where the
reference genome is used.


I have used BSgenpme and tried


sq<-as(seqinfo(Hsapiens), "GRanges")


counts<- loadAllData(files, sq, q = 10) but I got memory allocation error
Warning messages:
1: In structure(y, class = class(x), levels = levels(x)) :
  Reached total allocation of 3958Mb: see help(memory.size)
2: In structure(y, class = class(x), levels = levels(x)) :
  Reached total allocation of 3958Mb: see help(memory.size)
3: In structure(y, class = class(x), levels = levels(x)) :
  Reached total allocation of 3958Mb: see help(memory.size)
4: In structure(y, class = class(x), levels = levels(x)) :
  Reached total allocation of 3958Mb: see help(memory.size)
Error in unlist(sapply(1:nrow(regions), function(i) rep(regions$chr[i],  :
  error in evaluating the argument 'x' in selecting a method for function
'unlist': Error: cannot allocate vector of size 927.7 Mb
-----------------------------------------------------------


Shall i use the exome sequence only ??
Any help is highly appreciated
----------------------------------


 In deepSNV example


library(deepSNV)


regions <- data.frame(chr="B.FR.83.HXB2_LAI_IIIB_BRU_K034", start = 2074,
stop=3585)



## ------------------------------------------------------------------------

# HIVmix <- deepSNV(test = "
http://www.bsse.ethz.ch/cbg/software/deepSNV/data/test.bam",

#                   control = "
http://www.bsse.ethz.ch/cbg/software/deepSNV/data/control.bam",
#                   regions=regions, q=10)

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