srnadiffExp: Infrastructure for sRNA-Seq experiment and differential...

In mzytnicki/srnadiff: Finding differentially expressed unannotated genomic regions from RNA-seq data

Infrastructure for sRNA-Seq experiment and differential expression

Description

srnadiffExp is an S4 class providing the infrastructure (slots) to store the input data, methods parameters, intermediate calculations and results of a sRNA-diff approach.

Usage

srnadiffExp(
  bamFiles = NULL,
  sampleInfo = NULL,
  annotReg = NULL,
  diffMethod = NULL,
  normFactors = NULL
)

## S4 method for signature 'srnadiffExp'
show(object)

Arguments

bamFiles	A vector with the full paths to the BAM files.
sampleInfo	A data.frame with three columns labelled FileName, SampleName and Condition. The first column is the BAM file name (without extension), the second column the sample name, and the third column the condition to which sample belongs. Each row describes one sample.
annotReg	Optional annotation information. Annotated regions as a GRanges object. By example, ranges in the output from readAnnotation.
diffMethod	A character storing the name of the method used to compute the p-values. Can be DESeq2 (default), edgeR, or baySeq.
normFactors	A numeric vector, one size factor for each sample in the data.
object	An srnadiffExp object.

Details

srnadiffExp load and summarize sample BAM files into base-resolution coverage and estimate the size factors (the effective library size) from the coverage data.

To facilitate programming pipelines, NULL values are input for regions, parameters and countMatrix slots, in which case the default value is used as if the argument had been missing. These slots will be updated after differential expression (srnadiff) approach.

Value

srnadiffExp constructor returns an srnadiffExp object of class S4.

The show method informatively display object contents.

Slots

bamFiles

A BamFileList object with the full paths to the BAM files.

sampleInfo

A data.frame with sample and experimental design information. Each row describes one sample.

annotReg

A GRanges with annotation information.

diffMethod

A character storing the name of the method used to compute the p-values. Can be DESeq2, edgeR, or baySeq.

chromosomeSizes

A named vector with the sizes of the chromosomes.

coverages

The sample coverages, a named RleList object.

normFactors

A vector of normalization factors.

regions

A GenomicRanges of the candidate differentially expressed regions.

countMatrix

A matrix of non-negative integer count values, one row per region and one column per sample.

parameters

An named list. The parameters for the segmentation methods. See parameters.

Examples

basedir    <- system.file("extdata", package="srnadiff", mustWork = TRUE)
sampleInfo <- read.csv(file.path(basedir, "dataInfo.csv"))
gtfFile    <- file.path(basedir, "Homo_sapiens.GRCh38.76.gtf.gz")
annotReg   <- readAnnotation(gtfFile, feature="gene", source="miRNA")
bamFiles   <- file.path(basedir, sampleInfo$FileName)

srnaExp <- srnadiffExp(bamFiles, sampleInfo, annotReg)
srnaExp

mzytnicki/srnadiff documentation built on March 7, 2023, 2:18 a.m.