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

Description Usage Arguments Value

View source: R/methods.R

Description

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

Usage

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

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.

Value

A data frame.


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