add_2OmeScore: Add 2-O-methylation score to STORM-seq object

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

Add 2-O-methylation score to STORM-seq object

Description

Methylation score that considers the log2-FCH of start ratio between two RNA-seq libraries (low-dNTPs and high-dNTPs), subtracting the "noise" from a surrounding window.

Usage

add_2OmeScore(
  STORM,
  lib_LowdNTPs,
  lib_HighdNTPs,
  newColName = "auto",
  flankSize = 5,
  perNuc_Zscaling = F,
  onNucs = c("A", "C", "G", "T"),
  minCov = 50
)

Arguments

STORM	list. STORM object as output by storm_STORM
lib_LowdNTPs	character. Name of group with low-dNTPs library preparation found in STORM$META$group
lib_HighdNTPs	character. Name of group with high-dNTPs library preparation 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
flankSize	integer. Length of window to each side of position to consider for metric calculation
onNucs	character. Nucleotide(s) in which the metric will be calculated
minCov	integer. Minimal coverage in position for metric to be calculated

Details

Incarnato et al. 2017: For Nm Incarnato and collabs. used the fold change as the log2 of the ratio between the stoppage ratio at the low dNTPs concentration and the stoppage ratio in the high dNTPs concentration sample. Because the stoppage ratio seems to be strongly region specific, they subtracted the local background defined as the mean ratio of the stoppage in the neighborhood of a given position (+/- 5 nucleotides, excluding given position).

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