getIndexCoordinates

getIndexCoordinates,GenomicTiles-method

object

Additional arguments
Usually the original index or the chunk index.

A vector if tile ids. By default the complete index is returned.

A /codeGranges object representing an index of genomic positions.

index


Given an index of genomic positions, this method computes
the corresponding row positions in the assay


This package allows statistical analysis of genome-wide
data with smooth functions using generalized additive models
based on the implementation from the R-package 'mgcv'. It
provides methods for the statistical analysis of ChIP-Seq data
including inference of protein occupancy, and pointwise and
region-wise differential analysis. Estimation of dispersion and
smoothing parameters is performed by cross-validation. Scaling
of generalized additive model fitting to whole chromosomes is
achieved by parallelization over overlapping genomic intervals.

Georg Stricker

GenoGAM

A GAM based framework for analysis of ChIP-Seq data

getIndexCoordinates function

A /code{Granges} object representing an index of genomic positions.

Given an index of genomic positions, this method computes
the corresponding row positions in the assay

getIndexCoordinates: Compute the row coordinates for a given index

Description

Usage

Arguments

Value

Examples