choros | R Documentation |
This is a wrapper function to perform all the steps in the 'choros' pipeline: pre-processing of the RPF alignments, deciding which RPF lengths and frames to model, deciding which transcripts to use for training, regression modeling, correction of RPF counts, and evaluation of position-based biases before/after correction.
choros( bam_fname, transcript_fa_fname, transcript_length_fname, offsets_fname, expt_dir = ".", save_intermediate = T, extra_args = 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 offset / A site assignment rules .txt file |
expt_dir |
character; file path to directory to save output/intermediate files |
save_intermediate |
logical; whether to save intermediate files (if FALSE, only save alignment file with corrected weights) |
extra_args |
named list; additional parameters to pass onto internal functions |
A list containing: data frame of all RPF alignments with bias- corrected counts; data frame used for training the regression model; regression coefficients from the model fit; and a list of generated plots (diagnostic plot of RPF lengths and frames; bias evaluation per-codon and per-nucleotide position before and after bias correction)
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