add_CtoT_MRD: Add C-to-T misincorporation difference
In SchwartzLab/brainSTORM: brainSTORM. A package to process STORM-seq based data

add_CtoT_MRD

R Documentation

Add C-to-T misincorporation difference

Description

Calculates the difference of T conversion at C positions by subtracting the result of "T"/("T"+"C") between groups. Commonly NaCNBH3-Treated vs Control or vs Deacetylated negative control.

Usage

add_CtoT_MRD(
  STORM,
  group_A,
  group_B,
  newColName = "auto",
  onNucs = c("C"),
  minCov = 50
)

Arguments

`STORM`	list. STORM object as output by `storm_STORM`
`group_A`	character. Name of group to be compared as found in STORM$META$group
`group_B`	character. Name of group to be compared as found in STORM$META$group
`newColName`	character. Name of calculated metric to be stored in STORM$RES, assigned by default based on group_A and group_B
`onNucs`	character. Nucleotide(s) in which the metric will be calculated

Details

The reaction of ac4C with sodium cyanoborohydride (NaCNBH3) under acidic conditions forms the reduced nucleobase N4-acetyltetrahydrocytidine. The altered structure of this reduced nucleobase compared with ac4C causes the incorporation of non-cognate deoxynucleotide triphosphates (dNTPs) upon reverse transcription (Sas-Chen et al. 2020).

SchwartzLab/brainSTORM documentation built on May 14, 2022, 5:14 p.m.