Accessor variants slot in a SemplScores object

Usage

variants(x)

# S4 method for class 'SemplScores'
variants(x)

Arguments

x: a SemplScores object

Examples

library(VariantAnnotation)

# load default SEMs
data(sc)

# create a VRanges object
vr <- VRanges(seqnames = "chr12",
              ranges = 94136009, 
              ref = "G", alt = "C")

# calculate binding propensity
s <- scoreVariants(vr, sc, BSgenome.Hsapiens.UCSC.hg19::Hsapiens)

variants(s)
#> VRanges object with 1 range and 5 metadata columns:
#>       seqnames    ranges strand         ref              alt     totalDepth
#>          <Rle> <IRanges>  <Rle> <character> <characterOrRle> <integerOrRle>
#>   [1]    chr12  94136009      *           G                C           <NA>
#>             refDepth       altDepth   sampleNames softFilterMatrix |
#>       <integerOrRle> <integerOrRle> <factorOrRle>         <matrix> |
#>   [1]           <NA>           <NA>          <NA>                  |
#>                  upstream          downstream                ref_seq
#>               <character>         <character>            <character>
#>   [1] CCGTCAAGGAGAAGGCTTT AGGCATCTGCTGTTTTGTT CCGTCAAGGAGAAGGCTTTG..
#>                      alt_seq                 id
#>                  <character>        <character>
#>   [1] CCGTCAAGGAGAAGGCTTTC.. chr12:94136009:G>C
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
#>   hardFilters: NULL