resultlist: result object of runPanelcnMops - a list of instances of...

In panelcn.mops: CNV detection tool for targeted NGS panel data

Description

Result data included in panelcn.mops

Author(s)

Gundula Povysil

Examples

data(panelcn.mops)
resultlist

Example output

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

[[1]]

CNV regions: 
GRanges object with 11 ranges and 5 metadata columns:
       seqnames              ranges strand | SAMPLE1.bam SAMPLE4.bam
          <Rle>           <IRanges>  <Rle> |   <logical>   <logical>
   [1]        1   45794947-45805957      * |        <NA>        <NA>
   [2]        2   47596614-48034030      * |        <NA>        <NA>
   [3]        3   37035008-37092175      * |        <NA>        <NA>
   [4]        5 112090557-112179854      * |        <NA>        <NA>
   [5]        7    6012999-66460435      * |        <NA>        <NA>
   [6]       11 108098321-108236266      * |        <NA>        <NA>
   [7]       13   32890567-32972938      * |        <NA>        <NA>
   [8]       17    7572896-41276144      * |        <NA>        <NA>
   [9]       18   48573386-48604868      * |        <NA>        <NA>
  [10]       19     1206882-1226677      * |        <NA>        <NA>
  [11]       22   24129326-30090822      * |        <NA>        <NA>
       SAMPLE3.bam SAMPLE6.bam SAMPLE2.bam
         <logical>   <logical>   <logical>
   [1]        <NA>        <NA>        <NA>
   [2]        <NA>        <NA>        <NA>
   [3]        <NA>        <NA>        <NA>
   [4]        <NA>        <NA>        <NA>
   [5]        <NA>        <NA>        <NA>
   [6]        <NA>        <NA>        <NA>
   [7]        <NA>        <NA>        <NA>
   [8]        <NA>        <NA>        <NA>
   [9]        <NA>        <NA>        <NA>
  [10]        <NA>        <NA>        <NA>
  [11]        <NA>        <NA>        <NA>
  -------
  seqinfo: 11 sequences from an unspecified genome; no seqlengths

Individual CNVs: 
GRanges object with 1830 ranges and 4 metadata columns:
         seqnames            ranges strand |  sampleName       median
            <Rle>         <IRanges>  <Rle> |    <factor>    <numeric>
     [1]        1 45794947-45795140      * | SAMPLE1.bam -9.62540e-98
     [2]        1 45796157-45796260      * | SAMPLE1.bam -4.54174e-98
     [3]        1 45796823-45797037      * | SAMPLE1.bam -9.37054e-98
     [4]        1 45797061-45797259      * | SAMPLE1.bam -1.97034e-98
     [5]        1 45797302-45797552      * | SAMPLE1.bam -2.21065e-98
     ...      ...               ...    ... .         ...          ...
  [1826]       22 30069227-30069506      * | SAMPLE2.bam -1.69579e-98
  [1827]       22 30070794-30070961      * | SAMPLE2.bam  6.62660e-39
  [1828]       22 30074154-30074343      * | SAMPLE2.bam  3.71163e-86
  [1829]       22 30077397-30077621      * | SAMPLE2.bam -2.21856e-98
  [1830]       22 30090710-30090822      * | SAMPLE2.bam -3.59287e-98
                 mean        CN
            <numeric> <logical>
     [1] -9.62540e-98      <NA>
     [2] -4.54174e-98      <NA>
     [3] -9.37054e-98      <NA>
     [4] -1.97034e-98      <NA>
     [5] -2.21065e-98      <NA>
     ...          ...       ...
  [1826] -1.69579e-98      <NA>
  [1827]  6.62660e-39      <NA>
  [1828]  3.71163e-86      <NA>
  [1829] -2.21856e-98      <NA>
  [1830] -3.59287e-98      <NA>
  -------
  seqinfo: 11 sequences from an unspecified genome; no seqlengths

panelcn.mops documentation built on Nov. 8, 2020, 7:56 p.m.