indel_p_values: Compute the motif scores given a motif library and a list of...

Description Usage Arguments Details Value Author(s) Examples

View source: R/methods.R

Description

Compute the motif scores given a motif library and a list of

Usage

1
2
3
4
5
6
7
8
9
indel_p_values(
  motif_lib,
  indel_info,
  motif_scores,
  prior,
  trans_mat,
  sample_size,
  num_cores = 1
)

Arguments

motif_lib

A list of the position weight matrices for the motifs.

indel_info

A list object. Each element corresponds to an indel. See indel_info for details and an example.

motif_scores

A data frame in the same format as the output of indel_motif_scores.

prior

A numeric vector for the prior distribution parameters of

trans_mat

A numeric matrix for the transition matrix parameters

sample_size

An integer for the importance sampling sample size.

num_cores

An integer for the number of parallel processes.

Details

TODO.

Value

A list object of position weight matrices.

Author(s)

Qinyi Zhou qinyi.zhou@utdallas.edu, Chandler Zuo chandler.c.zuo@gmail.com, Sunyoung Shin sunyoung.shin@utdallas.edu

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
data(example)
motif_scores <- indel_motif_scores(motif_lib, indel_info)$list
indel_p_values(
  motif_lib=motif_lib,
  indel_info=indel_info,
  motif_scores=motif_scores,
  prior=prior,
  trans_mat=trans_mat,
  sample_size=100,
  num_cores=1
)

chandlerzuo/atIndel documentation built on Aug. 20, 2021, 6:33 p.m.