add_CytPer: Add cytidine persistance index to STORM object

In SchwartzLab/brainSTORM: brainSTORM. A package to process STORM-seq based data

Add cytidine persistance index to STORM object

Description

Cytidine score modified from (Squires et al. 2012). It accounts for positions with Thymine reads in Cytidine positions in the Control/Mock sample. CytPer = (C_bisulphite / (C_bisulphite + T_bisulphite)) - (1 - (C_control / C_control + T_control))

Usage

add_CytPer(
  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

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