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

View source: R/metrics.R

add_2OmeScoreR Documentation

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.