parameters_are_good: Check input parameters.

Description Usage Arguments Value

View source: R/func.R

Description

Check input parameters.

Usage

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parameters_are_good(annot, count_data_A, count_data_B, boot_data_A, boot_data_B,
  TARGET_COL, PARENT_COL, correction, testmode, scaling, threads, seed,
  p_thresh, abund_thresh, dprop_thresh, qboot, qbootnum, qrep_thresh, rboot,
  rrep_thresh, reckless)

Arguments

annot

Annotation dataframe.

count_data_A

A dataframe of estimated counts.

count_data_B

A dataframe of estimated counts.

boot_data_A

A list of dataframes, one per sample, each with all the bootstrapped estimates for the sample.

boot_data_B

A list of dataframes, one per sample, each with all the bootstrapped estimates for the sample.

TARGET_COL

Name of transcript id column in annotation.

PARENT_COL

Name of gene id column in annotation.

correction

P-value correction method.

testmode

Which test to run.

scaling

Abundance scaling factor.

threads

Number of threads.

seed

Seed for random engine.

p_thresh

Significance level.

abund_thresh

Minimum transcript abundance per sample.

dprop_thresh

Minimum change in proportion.

qboot

Whether to bootstrap against quantifications.

qbootnum

Number of bootstrap iterations.

qrep_thresh

Confidence threshold.

rboot

Whether to bootstrap against samples.

rrep_thresh

Confidence threshold.

reckless

whether to ignore detected annotation discrepancies

Value

List:


bartongroup/RATS documentation built on May 21, 2018, 4:42 a.m.