dataFrame-methods: Construct a data.frame from genomic data for plotting

In SNPchip: Visualizations for copy number alterations

Description

Construct a data.frame of genomic data (log R ratios and BAFs) from a RangedSummarizedExperiment with markers in the interval given by the GRanges object.

Methods

signature(range = "GRanges", data = "gSet")

The argument range is often intervals from a hidden Markov model fit to the genomic data in the data object. gSet-derived classes contain assay data on copy number and allele frequencies.

signature(range = "GRanges", data = "RangedSummarizedExperiment")

The argument range is often intervals from a hidden Markov model fit to the genomic data in the data object. The RangedSummarizedExperiment is assumed to contain log R ratio (lrr) and B allele frequency (baf) assays.

SNPchip documentation built on Oct. 31, 2019, 2:07 a.m.