Rapidr invalid class “SummarizedExperiment”

[paumarc]

Hello everybody,

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?

thanks


> 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:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=hr_HR.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=hr_HR.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=hr_HR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=hr_HR.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.36.3
[3] rtracklayer_1.28.10 Biostrings_2.36.4
[5] XVector_0.8.0 GenomicRanges_1.20.6
[7] GenomeInfoDb_1.4.2 IRanges_2.2.7
[9] S4Vectors_0.6.5 BiocGenerics_0.14.0
[11] RAPIDR_0.1.1

loaded via a namespace (and not attached):
[1] Rcpp_0.12.1 magrittr_1.5 zlibbioc_1.14.0
[4] GenomicAlignments_1.4.1 BiocParallel_1.2.21 stringr_1.0.0
[7] plyr_1.8.3 tools_3.2.2 data.table_1.9.4
[10] lambda.r_1.1.7 futile.logger_1.4.1 reshape2_1.4.1
[13] PropCIs_0.2-5 futile.options_1.0.0 bitops_1.0-6
[16] RCurl_1.95-4.7 stringi_0.5-5 Rsamtools_1.20.4
[19] XML_3.98-1.3 chron_2.3-47
>

[Manonathan]

Rapidr

Hi,
Use this command
makeBinnedCountsFile(c("trisomie_sorted.bam"), c("SRR611850"), 'output.fname', k = 20000)
Before running the command please index bam file and keep the index(.bai)
in the same folder.

[paumarc]

thanks for your help

pau

[Greeshma Thulasi]

Hi,
I think this is very late in this discussion!
I am confused that, our reference set should be of known samples, which requires normal as well as abnormal samples?