GenoGAMDataSet-metrics: Computing metrics

In gstricker/fastGenoGAM: A GAM based framework for analysis of ChIP-Seq data

Description

Computing metrics on each tile of the GenoGAMDataSet object. All metrics from the Summary generics group, as well as mean, var, sd, median, mad and IQR are supported.

Usage

## S4 method for signature 'GenoGAMDataSet'
Summary(x, ..., na.rm = FALSE)

## S4 method for signature 'GenoGAMDataSet'
mean(x)

## S4 method for signature 'GenoGAMDataSet,ANY'
var(x)

## S4 method for signature 'GenoGAMDataSet'
sd(x)

## S4 method for signature 'GenoGAMDataSet'
median(x)

## S4 method for signature 'GenoGAMDataSet'
mad(x)

## S4 method for signature 'GenoGAMDataSet'
IQR(x)

## S4 method for signature 'GenoGAMDataSetList'
mean(x)

## S4 method for signature 'GenoGAMDataSetList,ANY'
var(x)

## S4 method for signature 'GenoGAMDataSetList'
sd(x)

## S4 method for signature 'GenoGAMDataSetList'
median(x)

## S4 method for signature 'GenoGAMDataSetList'
mad(x)

## S4 method for signature 'GenoGAMDataSetList'
IQR(x)

Arguments

x	A GenoGAMDataSet object
...	Additional arguments
na.rm	Should NAs be dropped. Otherwise the result is NA

Value

A matrix with the specified metric computed per tile per column of the assay data.

Author(s)

Georg Stricker [e-mail]

Examples

ggd <- makeTestGenoGAMDataSet()
sum(ggd)
min(ggd)
max(ggd)
mean(ggd)
var(ggd)
sd(ggd)
median(ggd)
mad(ggd)
IQR(ggd)

gstricker/fastGenoGAM documentation built on May 17, 2019, 8:56 a.m.