control: GRanges object of countWindows with read counts for control...
In panelcn.mops: CNV detection tool for targeted NGS panel data

Description Details Author(s) Examples

The object was created using the function countBamListInGRanges with the enclosed countWindows object, a subset of BAM files provided by the 1000 Genomes Project and the read.width parameter set to 150.

Control data included in panelcn.mops

Gundula Povysil

1 2	data(panelcn.mops) control

Loading required package: cn.mops
Loading required package: parallel
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb

Attaching package: ‘cn.mops’

The following object is masked from ‘package:S4Vectors’:

    params

GRanges object with 370 ranges and 5 metadata columns:
        seqnames            ranges strand | SAMPLE2.bam SAMPLE3.bam SAMPLE4.bam
           <Rle>         <IRanges>  <Rle> |   <integer>   <integer>   <integer>
    [1]        1 45794947-45795140      * |         447         671         657
    [2]        1 45796157-45796260      * |         314         445         349
    [3]        1 45796823-45797037      * |         289         479         464
    [4]        1 45797061-45797259      * |         241         367         366
    [5]        1 45797302-45797552      * |         298         520         450
    ...      ...               ...    ... .         ...         ...         ...
  [366]        2 48032018-48032197      * |         518         752         648
  [367]        2 48032726-48032877      * |         151         180         212
  [368]        2 48033312-48033528      * |         511         660         668
  [369]        2 48033560-48033821      * |         598         785         695
  [370]        2 48033887-48034030      * |         469         625         598
        SAMPLE5.bam SAMPLE6.bam
          <integer>   <integer>
    [1]         556         579
    [2]          40         312
    [3]         339         355
    [4]         306         274
    [5]         303         382
    ...         ...         ...
  [366]         209         544
  [367]         256         127
  [368]         238         503
  [369]         368         613
  [370]         173         537
  -------
  seqinfo: 11 sequences from an unspecified genome; no seqlengths