pvalue_single_thread_helper: Compute the p-values for score change for a single motif and...

In chandlerzuo/atIndel: Affinity test for identifying regularity Indels

Compute the p-values for score change for a single motif and a set of indels with the same insertion length.

Description

Compute the p-values for score change for a single motif and a set of indels with the same insertion length.

Usage

pvalue_single_thread_helper(
  pwm,
  motif_name,
  indel_info,
  motif_scores,
  prior,
  trans_mat,
  sample_size,
  normalize_score_by_seq_len
)

Arguments

pwm	A numeric matrix for the position weight matrix of the motif.
motif_name	A character for the motif name.
indel_info	A list for information related to indels. See the argument for indel_p_values for more details.
motif_scores	A numeric matrix including two column. The first column is the scores for the longer sequences. The 2nd column is the scores for the shorter sequences. Each row corresponding to one indel.
prior	A numeric vector for the prior of the Markov Chain background model.
trans_mat	A numeric matrix for the transition matrix of the Markov Chain background model.
sample_size	An integer for the Monte-Carlo sample size.
normalize_score_by_seq_len	Boolean for whether scores are normalized by sequence lengths.

Value

A data frame.

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