I am trying to set up a pipeline to aneuploidy prenatal diagnostic. In order to perform the analysis, I am using rapidR.
To create a binned bound file from BAM's, I do;
makeBinnedCountsFile(bam.file.list = c("trisomie_sorted.bam"), sampleIDs = c("SRR611850"), binned.counts.fname = output.fname, k = 20000)
first would like to know what is the parameter ki, at the manual it is defined ask is the bin size, default is 20000 kb, is it the size of the bam file (binary) in kb?
When I execute the command above I got the following error:
> makeBinnedCountsFile(bam.file.list = c("trisomie_sorted.bam"), sampleIDs = c("SRR611850"), binned.counts.fname = output.fname, k = 20000) Binning counts in bam files doing the binning Error in validObject(.Object) : invalid class “SummarizedExperiment” object: 'rowRanges' length differs from 'assays' nrow
Can anybody tell me how to deal with it? There is some tutorial (with bam files included) to learn how to use RapidR?
> sessionInfo() R version 3.2.2 (2015-08-14) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.3 LTS locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=hr_HR.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=hr_HR.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=hr_HR.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=hr_HR.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats4 parallel stats graphics grDevices utils datasets  methods base other attached packages:  BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.36.3  rtracklayer_1.28.10 Biostrings_2.36.4  XVector_0.8.0 GenomicRanges_1.20.6  GenomeInfoDb_1.4.2 IRanges_2.2.7  S4Vectors_0.6.5 BiocGenerics_0.14.0  RAPIDR_0.1.1 loaded via a namespace (and not attached):  Rcpp_0.12.1 magrittr_1.5 zlibbioc_1.14.0  GenomicAlignments_1.4.1 BiocParallel_1.2.21 stringr_1.0.0  plyr_1.8.3 tools_3.2.2 data.table_1.9.4  lambda.r_1.1.7 futile.logger_1.4.1 reshape2_1.4.1  PropCIs_0.2-5 futile.options_1.0.0 bitops_1.0-6  RCurl_1.95-4.7 stringi_0.5-5 Rsamtools_1.20.4  XML_3.98-1.3 chron_2.3-47