tagClustersQuantile: Quantile metadata stored in CAGEr objects.

In CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Description

Accessor functions to quantile metadata.

Usage

tagClustersQuantile(object, samples = NULL, q = NULL)

## S4 method for signature 'TagClusters'
tagClustersQuantile(object, samples = NULL,
  q = NULL)

## S4 method for signature 'CAGEexp'
tagClustersQuantile(object, samples = NULL,
  q = NULL)

tagClustersQuantileLow(object, samples = NULL, q = NULL)

## S4 method for signature 'CAGEset'
tagClustersQuantileLow(object, samples = NULL,
  q = NULL)

## S4 method for signature 'CAGEexp'
tagClustersQuantileLow(object, samples = NULL,
  q = NULL)

tagClustersQuantileUp(object, samples = NULL, q = NULL)

## S4 method for signature 'CAGEset'
tagClustersQuantileUp(object, samples = NULL,
  q = NULL)

## S4 method for signature 'CAGEexp'
tagClustersQuantileUp(object, samples = NULL,
  q = NULL)

tagClustersQuantileLow(object, samples = NULL) <- value

## S4 replacement method for signature 'CAGEset'
tagClustersQuantileLow(object,
  samples = NULL) <- value

## S4 replacement method for signature 'CAGEexp'
tagClustersQuantileLow(object,
  samples = NULL) <- value

tagClustersQuantileUp(object, samples = NULL) <- value

## S4 replacement method for signature 'CAGEset'
tagClustersQuantileUp(object,
  samples = NULL) <- value

## S4 replacement method for signature 'CAGEexp'
tagClustersQuantileLow(object,
  samples = NULL) <- value

Arguments

object	A CAGEr object.
samples	Sample name(s), number(s) or NULL (default) for all samples.
q	A single quantile (not a list)
value	A list (one entry per sample) of data frames with multiple columns: cluster for the cluster ID, and then q_0.n where 0.n indicates a quantile.

Value

Returns a data.frame where the first column gives cluster names and the next columns give quantile positions, in zero-based chromosome coordinates (because the tag clusters in CAGEset objects are represented in zero-based coordinates as well)).

CAGEr documentation built on Jan. 17, 2021, 2 a.m.