Load tantan results
loadTantan.RdLoad the output of tantan -f4 | awk 'OFS="\t" {print $1, $2, $3, $6, $5, "."}.
Arguments
- file
The output file to load
- genome.file
Path to the genome file that was given to
tantan- genome.name
A genome name for the
seqinfoof the returnedGRanges
Value
A GenomicRanges::GRanges object.
Details
If given the genome file that tantan used, it will use it to create a
seqinfo object for the returned GRanges object
Examples
loadTantan(system.file('extdata/example.bed.xz', package="changchang"))
#> GRanges object with 1000 ranges and 3 metadata columns:
#> seqnames ranges strand | score
#> <Rle> <IRanges> <Rle> | <numeric>
#> [1] 1086a8205b 1-613 + | 102.66700
#> [2] 1086a8205b 645-767 + | 3.42857
#> [3] 1086a8205b 766-6420 + | 106.67900
#> [4] 1086a8205b 7381-7473 + | 2.26829
#> [5] 1086a8205b 8178-8206 - | 2.23077
#> ... ... ... ... . ...
#> [996] 1086a8205b 1706037-1706047 - | 5.50000
#> [997] 1086a8205b 1706066-1706079 - | 2.80000
#> [998] 1086a8205b 1706963-1706986 + | 3.25000
#> [999] 1086a8205b 1707022-1707042 + | 4.20000
#> [1000] 1086a8205b 1707081-1707106 + | 2.16667
#> normTandem nchar
#> <factor> <integer>
#> [1] AACCCT 6
#> [2] AACCCTAACCCTAACCCTAACCCTAACCCTAACCT 35
#> [3] AAACCTAGCGACAACACAGGGAGAACACTCTCACCTTAACAAGAACCCTTATT 53
#> [4] AAAATTTTGCGCGGTTGCGGGCGGGCGCGGGGGCCGATTCC 41
#> [5] ACGGGCGGGGGCC 13
#> ... ... ...
#> [996] CG 2
#> [997] AAAAC 5
#> [998] ACTAGCC 7
#> [999] AGCCT 5
#> [1000] AAAAAACTAGCC 12
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths