Convert data.table to GenomicRanges Object

Single command to smartly convert a data.table object to a GenomicRanges object by wrapping gr_refactor_seqs() around the gUtils::dt2gr() to avoid seqinfo conflicts and apply proper sorting.

Usage

dt_to_gr(input_dt)

Arguments

input_dt

data.table object that minimally contains columns like chromosome start, and end position that describe the genomic coordinates of the range

Value

GenomicRanges object with input columns and updated seqinfo, seqnames, seqlengths, seqlevels

Examples

# Converting from data.table to GenomicRanges can be easily done with gUtils::dt2gr()
# however this single command conversion leaves some loose ends with the seqinfo

# Look at the original data.table
braf_dnase_demo_dt_hg38
#>    seqnames     start       end strand signalValue  pValue biospecimen   gene
#>      <char>     <int>     <int> <char>       <num>   <num>      <char> <char>
#> 1:     chr7 140740305 140740552      *     2.16924 1.59134        K562   KRAS
#> 2:     chr7 140797423 140798072      *     2.17796 1.59886        K562   KRAS
#> 3:     chr7 140826433 140826768      *     2.59020 1.98645        K562   KRAS
#> 4:     chr7 140842477 140843425      *     6.56378 7.66134        K562   KRAS
# Now convert to GRanges
dt_to_gr(braf_dnase_demo_dt_hg38)
#> GRanges object with 4 ranges and 4 metadata columns:
#>       seqnames              ranges strand | signalValue    pValue biospecimen
#>          <Rle>           <IRanges>  <Rle> |   <numeric> <numeric> <character>
#>   [1]     chr7 140740305-140740552      * |     2.16924   1.59134        K562
#>   [2]     chr7 140797423-140798072      * |     2.17796   1.59886        K562
#>   [3]     chr7 140826433-140826768      * |     2.59020   1.98645        K562
#>   [4]     chr7 140842477-140843425      * |     6.56378   7.66134        K562
#>              gene
#>       <character>
#>   [1]        KRAS
#>   [2]        KRAS
#>   [3]        KRAS
#>   [4]        KRAS
#>   -------
#>   seqinfo: 24 sequences from GRCh38 genome
# Check the seqinfo
GenomeInfoDb::seqinfo(dt_to_gr(braf_dnase_demo_dt_hg38))
#> Seqinfo object with 24 sequences from GRCh38 genome:
#>   seqnames seqlengths isCircular genome
#>   chr1      248956422      FALSE GRCh38
#>   chr2      242193529      FALSE GRCh38
#>   chr3      198295559      FALSE GRCh38
#>   chr4      190214555      FALSE GRCh38
#>   chr5      181538259      FALSE GRCh38
#>   ...             ...        ...    ...
#>   chr20      64444167      FALSE GRCh38
#>   chr21      46709983      FALSE GRCh38
#>   chr22      50818468      FALSE GRCh38
#>   chrX      156040895      FALSE GRCh38
#>   chrY       57227415      FALSE GRCh38

# Compared to the old way
# Conversion looks fine
gUtils::dt2gr(braf_dnase_demo_dt_hg38)
#> GRanges object with 4 ranges and 4 metadata columns:
#>       seqnames              ranges strand | signalValue    pValue biospecimen
#>          <Rle>           <IRanges>  <Rle> |   <numeric> <numeric> <character>
#>   [1]     chr7 140740305-140740552      * |     2.16924   1.59134        K562
#>   [2]     chr7 140797423-140798072      * |     2.17796   1.59886        K562
#>   [3]     chr7 140826433-140826768      * |     2.59020   1.98645        K562
#>   [4]     chr7 140842477-140843425      * |     6.56378   7.66134        K562
#>              gene
#>       <character>
#>   [1]        KRAS
#>   [2]        KRAS
#>   [3]        KRAS
#>   [4]        KRAS
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome
# However the seqinfo will conflict with other hg38 GRanges
GenomeInfoDb::seqinfo(gUtils::dt2gr(braf_dnase_demo_dt_hg38))
#> Seqinfo object with 1 sequence from an unspecified genome:
#>   seqnames seqlengths isCircular genome
#>   chr7      140843425         NA   <NA>