addDiffStatus-methods: Add a status column

In steveped/extraChIPs: Additional functions for working with ChIP-Seq data

Add a status column

Description

Add a status column based on significance and estimated change

Usage

addDiffStatus(x, ...)

## S4 method for signature 'data.frame'
addDiffStatus(
  x,
  fc_col = "logFC",
  sig_col = c("FDR", "hmp_fdr", "p_fdr", "adj.P.Value"),
  alpha = 0.05,
  cutoff = 0,
  up = "Increased",
  down = "Decreased",
  other = "Unchanged",
  missing = "Undetected",
  new_col = "status",
  drop = FALSE,
  ...
)

## S4 method for signature 'DataFrame'
addDiffStatus(x, new_col = "status", ...)

## S4 method for signature 'GRanges'
addDiffStatus(x, ...)

## S4 method for signature 'GRangesList'
addDiffStatus(x, ...)

## S4 method for signature 'SummarizedExperiment'
addDiffStatus(x, ...)

Arguments

x	Object to be classified
...	Used to pass arguments between methods
fc_col	Name of the fold-change column
sig_col	Name of the column with significance values
alpha	significance threshold
cutoff	minimum estimated change to be considered in either of the up or down categories
up, down, other	factor levels to annotate regions based on the above criteria
missing	Value to add when either fc_col or sig_col has NA values
new_col	name of the new column to be added
drop	logical(1) Drop unused factor levels from the status column

Details

This takes a simple object and adds a new column classifying entries into one of three categories, as specified using up, down or other. Results in the new column will always be returned as a factor with levels in order of the values provided in the arguments other, down and up

Value

An object of the same type as provided

Examples

## Working with a data.frame
set.seed(101)
df <- data.frame(logFC = rnorm(20), p = rbeta(20, shape1 = 1, shape2 = 20))
df$FDR <- p.adjust(df$p, "fdr")
addDiffStatus(df)

## This works identically with a GRanges object, amongst others
gr <- GRanges(paste0("chr1:", seq_len(20)))
mcols(gr) <- df
addDiffStatus(gr)

steveped/extraChIPs documentation built on Aug. 1, 2024, 12:36 a.m.