load_bam | R Documentation |
This function takes a .bam alignment file where each row corresponds to an individual RPF read; generates annotations for RPF codon index, 5' digest length, 3' digest length, A-/P-/E-site codons, GC content, and bias sequences; filters out invalid RPFs; and aggregates identical RPFs.
If 'read_type' is 'disome', user must also specify 'offsets_5prime_fname' and 'offsets_3prime_fname'.
load_bam( bam_fname, transcript_fa_fname, transcript_length_fname, offsets_fname = NULL, num_cores = NULL, gc_omit = "APE", read_type = "monosome", f5_length = 3, f3_length = 3, offsets_5prime_fname = NULL, offsets_3prime_fname = NULL )
bam_fname |
character; file path to .bam alignment file |
transcript_fa_fname |
character; file path to transcriptome .fasta file |
transcript_length_fname |
character; file path to transcriptome lengths file |
offsets_fname |
character; file path to A-site assignment rules file |
num_cores |
integer; number of cores to use for parallelization |
read_type |
character; one of 'monosome' or 'disome' |
f5_length |
integer; length of sequence between RPF 5' end and A site |
f3_length |
integer; length of sequence between A site and RPF 3' end |
A data frame of aggregated RPF counts and annotations
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