get_bias_seq | R Documentation |
A function to pull the nucleotides at the ends of a ribosome-protected fragment, defined by ribosome position and size.
get_bias_seq( dat, transcript_seq, bias_region, bias_length = 3, read_type = "monosome" )
dat |
data frame containing columns 'transcript', 'd5', 'd3', 'utr5_length', and codon indices. |
transcript_seq |
character; output from 'load_fasta' |
bias_region |
character; one of ‘f5' or 'f3' corresponding to 5’ or 3' bias sequence |
bias_length |
integer; number of nucleotides to include in bias sequence |
read_type |
character; one of 'monosome' or 'disome' |
If 'read_type' is 'monosome', then A site codon indices should be named 'cod_idx' in 'dat'. If 'read_type' is 'disome', then A site codon indices should be named 'cod_idx_lagging' and 'cod_idx_leading' in 'dat'.
A character vector corresponding to rows of 'dat'
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