init_data | R Documentation |
This function enumerates data points to train a regression model of RPF counts, given a list of transcripts for training
init_data( transcript_fa_fname, transcript_length_fname, digest5_lengths = 15:18, digest3_lengths = 9:11, d5_d3_subsets = NULL, f5_length = 3, f3_length = 3, num_cores = NULL, which_transcripts = NULL, exclude_codons5 = 10, exclude_codons3 = 10, compute_gc = T, gc_omit = "APE" )
transcript_fa_fname |
character; file path to transcriptome .fasta file |
transcript_length_fname |
character; file path to transcriptome lengths file |
digest5_lengths |
integer vector; legal 5' digest lengths |
digest3_lengths |
integer vector; legal 3' digest lengths |
d5_d3_subsets |
data frame; columns of 'd5' and 'd3' to initiate data over |
f5_length |
integer; length of 5' bias sequence |
f3_length |
integer; length of 3' bias sequence |
num_cores |
integer; number of cores to use for parallelization |
which_transcripts |
character vector; transcripts selected for regression |
exclude_codons5 |
integer; number of codons to exclude from 5' end of transcript |
exclude_codons3 |
integer; number of codons to exclude from 3' end of transcript |
compute_gc |
logical; whether to return RPF GC-content |
gc_omit |
character; one of 'A', 'AP', or 'APE' codons to omit for GC-content calculation |
data frame of data to use for downstream regression modeling
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.