load_lengths | R Documentation |
'load_lengths' reads in a transcriptome lengths file
‘gff_to_lengths' reads in a GFF-formatted file and parse for 5’ UTR, CDS, and 3' UTR lengths. First column must be the transcript name; third column must be one of 'UTR5', 'CDS', or 'UTR3'.
'load_fasta' reads in a FASTA-formatted file and generates a character vector of transcript sequences
'load_offsets' reads in a .txt file containing A-site offset values per RPF length and frame. Row names correspond to RPF length and column names correspond to RPF frame (named 'frame_0', 'frame_1', and 'frame_2').
'read_fasta_as_codons' reads in a FASTA-formatted file and generates a list of character vectors where transcript sequences have been split into codons.
load_lengths(lengths_fname) gff_to_lengths(gff_fname) load_fasta(transcript_fa_fname) load_offsets(offsets_fname) read_fasta_as_codons(transcript_fa_fname, transcript_length_fname)
gff_fname |
character; file path to GFF annotation file |
transcript_fa_fname |
character; file path to transcriptome .fasta file |
offsets_fname |
character; file path to A site assignment rules .txt file |
transcript_length_fname |
character; file path to transcriptome lengths file |
length_fname |
character; file path to transcriptome lengths file |
A data frame containing transcript names, 5' UTR lengths, CDS lengths, and 3' UTR lengths
A data frame containing transcript names, 5' UTR lengths, CDS
A named numeric vector of transcript sequences
A data frame in long format of A site offset values per RPF length and frame
A named list of character vectors of transcript sequences as codons
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