compareSamples: Compare Samples using Fisher's exact test

In LihuaJulieZhu/GUIDEseq: GUIDE-seq and PEtag-seq analysis pipeline

Compare Samples using Fisher's exact test

Description

Compare Samples using Fisher's exact test

Usage

compareSamples(
  df,
  col.count1,
  col.count2,
  total1,
  total2,
  multiAdjMethod = "BH",
  comparison.score = c("peak_score", "umi.count")
)

Arguments

df	a data frame containing the peak score and sequence depth for each sample
col.count1	the score (e.g., peak_score) column used as the numerator for calculating odds ratio. For example,if the tenth column contains the score for sample 1, then set col.count1 = 10
col.count2	the score (e.g., peak_score) column used as the denominator for calculating odds ratio. For example,if the nineteenth column contains the score for sample 1, then set col.count2 = 19
total1	the sequence depth for sample 1
total2	the sequence depth for sample 2
multiAdjMethod	A vector of character strings containing the names of the multiple testing procedures for which adjusted p-values are to be computed. This vector should include any of the following: "none", "Bonferroni", "Holm", "Hochberg", "SidakSS", "SidakSD", "BH", "BY", "ABH", and "TSBH". Please type ?multtest::mt.rawp2adjp for details. Default to "BH"
comparison.score	the score to be used for statistical analysis. Two options are available: "peak_score" and "umi.count" umi.count is the number of unique UMIs in the associated peak region without considering the sequence coordinates while peak_score takes into consideration of the sequence coordinates

Author(s)

Lihua Julie Zhu

LihuaJulieZhu/GUIDEseq documentation built on March 27, 2024, 9:42 p.m.