df.to.gr: Convert a data.frame to a GRanges object

In NGScopy: NGScopy: Detection of Copy Number Variations in Next Generation Sequencing sequencing

Description

Convert a data.frame to a GRanges object

Usage

df.to.gr(x, which.chr = "chr", which.start = "start", which.end = "end",
  which.width = "width", which.name = "name", chrlength = NULL,
  start0 = TRUE)

Arguments

x	data.frame or matrix
which.chr	character, the column name of 'chr'
which.start	character, the column name of 'start'
which.end	character, the column name of 'end'
which.width	character, the column name of 'width'
which.name	character, the column name of 'name'
chrlength	numeric, the lengths of the chromosomes
start0	logical, wheter the 'start' is 0-based.

Value

a GRanges object

Author(s)

Xiaobei Zhao

Examples

## Not run: 
x <- data.frame(
  chr=c('chr1','chr2'),start=0,end=100,
  name=paste0('ID',1:2),score=1:2
  )
df.to.gr(x)
df.to.gr(x,chrlength=c(chr1=1000,chr2=1200))

## End(Not run)

Example output

Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

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':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    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
GRanges object with 2 ranges and 1 metadata column:
Found more than one class "List" in cache; using the first, from namespace 'Xmisc'
Also defined by 'S4Vectors'
      seqnames    ranges strand |     score
         <Rle> <IRanges>  <Rle> | <integer>
  ID1     chr1  [1, 100]      * |         1
  ID2     chr2  [1, 100]      * |         2
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths
GRanges object with 2 ranges and 1 metadata column:
Found more than one class "List" in cache; using the first, from namespace 'Xmisc'
Also defined by 'S4Vectors'
      seqnames    ranges strand |     score
         <Rle> <IRanges>  <Rle> | <integer>
  ID1     chr1  [1, 100]      * |         1
  ID2     chr2  [1, 100]      * |         2
  -------
  seqinfo: 2 sequences from an unspecified genome

NGScopy documentation built on May 6, 2019, 2:43 a.m.