add_scoreC3p: Add ScoreC accounting for read-stops (3prime)
In SchwartzLab/brainSTORM: brainSTORM. A package to process STORM-seq based data

add_scoreC3p

R Documentation

Add ScoreC accounting for read-stops (3prime)

Add ScoreC accounting for read-stops (3prime)

add_scoreC3p(
  STORM,
  group_A,
  newColName = "auto",
  onNucs = c("A", "C", "G", "T"),
  minMedCov = 30,
  flankSize = 6,
  minReads = 50
)

`STORM`	list. STORM object as output by `storm_STORM`
`group_A`	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
`minMedCov`	integer. Minimal median coverage of window around position, delimited by flankSize
`flankSize`	integer. Length of window to each side of position to consider for metric calculation
`minReads`	integer. Minimum number of reads needed at site neighborhood to calculate the score.