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

In chandlerzuo/atIndel: Affinity test for identifying regularity Indels

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

Description

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

Usage

indel_p_values(
  motif_lib,
  indel_info,
  motif_scores,
  prior,
  trans_mat,
  sample_size,
  normalize_score_by_seq_len,
  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.
normalize_score_by_seq_len	Boolean for whether the scores are normalized by the sequence lengths.
num_cores	An integer for the number of parallel processes.

Details

TODO.

Value

A list object of position weight matrices.

Author(s)

Qinyi Zhou [e-mail], Chandler Zuo [e-mail], Sunyoung Shin [e-mail]

Examples

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,
  normalize_score_by_seq_len=FALSE,
  num_cores=1
)

chandlerzuo/atIndel documentation built on Jan. 20, 2024, 4:10 a.m.