Quaffle: Run Quaffle

In fursham-h/quafle: Quantifying Usage of Alternative First and Last Exons

Run Quaffle

Description

'Quaffle' will identify all alternative first and last (AFL) exons and quantify the length-normalized read counts for each sample. This function require a reference GTF file from which an AFL database is built upon, and a directory containing aligned read files (BAMs). 'Quaffle' outputs a RangedSummarizedExperiment object that stores AFL coordinates, normalized read counts and sample metadata

Usage

Quaffle(bamdir, gtf, colData = NULL)

Arguments

bamdir	Directory containing BAM files and indices
gtf	Path to reference GTF file
colData	Optional: A dataframe containing names of samples as rownames and other sampel information

Value

RangedSummarizedExperiment object, with 2 assays; inc and total normalized read counts. Number of columns in object equals to number of samples/BAM files and number of rows equals to number of identified alternative First and Last exons.

Examples

library(quaffle)
gtf <- system.file("extdata/wtap.gtf", package = "quaffle")
bams <- system.file("extdata/bams", package = "quaffle")

se <- Quaffle(bams, gtf)

fursham-h/quafle documentation built on Oct. 9, 2022, 4:49 p.m.