attribute_sequence_contex_indel {YAPSA} | R Documentation |
The function is a wrapper and uses getSequenceContext
to annotate the sequence context.
attribute_sequence_contex_indel( in_dat, in_REF.field = "REF", in_ALT.field = "ALT", in_verbose = FALSE, in_offsetL = 10, in_offsetR = 50 )
in_dat |
VRanges object or data frame which carries one column for the reference base and one column for the variant base |
in_REF.field |
String indicating which column of |
in_ALT.field |
String indicating which column of |
in_verbose |
Verbose if |
in_offsetL |
Number of nucleotides which should be annotated downstream of the variant. Per default 10 bps are annotated |
in_offsetR |
Number of nucleotides which should be annotated upstream of the catiant. Per default 50 bps are annotated |
VRanges object or data frame with the same number rows and additional
columns containing the type of INDEL (Ins = insertion and Del = deletion),
the annotated sequence context of the defined length, the absolute number of
exchanged nucleotides and the nucleotide exchange between in_REF.field
and in_ALT.field
.
data(GenomeOfNl_raw) GenomeOfNl_context <- attribute_sequence_contex_indel( in_dat = head(GenomeOfNl_raw), in_REF.field = "REF", in_ALT.field = "ALT", in_verbose = FALSE, in_offsetL= 10, in_offsetR=50) GenomeOfNl_context