RNAseq (version 0.1.1)

downstream-utils: Utilities for downstream analysis

Description

WARNING! CONSTRUCTION AREA.

Utility functions used for some basic downstream (i.e. post matching) analysis.

Usage

buildAFMtable(FMtable, genes)

Arguments

FMtable

An FM table (Fragmented Match table) like the one produced by the matchRNAtoGenome function.

genes

A data.frame like the geneMouse data set found in the GenomicFeatures package.

Details

buildAFMtable builds an AFM table (Annotated Fragmented Match table). This table is obtained by appending the "genes" column to the input FM table. This column contains the names of the genes assigned to each match (1 match per row). buildAFMtable takes between 4 and 5 min. when called on an FM table with 0.5 million rows and the geneMouse data set.

See Also

matchRNAtoGenome, geneMouse

Examples

if (interactive()) {
    example(matchRNAtoGenome)
    load(file.path(tempdir(), "FMtable.rda"))
    library(GenomicFeatures)
    data(geneMouse)
    AFMtable <- buildAFMtable(FMtable, geneMouse)
  }