ICASDataSet: ICASDataSet object and constructors

In tangchao7498/ICAS:

Description

The ICASDataSet object is the center of Intron Centric Alternative Splicing (ICAS) analysis. It stores all information associated with the dataset, including raw data, PSI, annotations, analyes, etc. All that is needed to construct a ICASDataSet object is an Splice Junction (SJ) expression matrix (rows are SJ, columns are cells), and GTF file which have been used in STAR (which we strongly recommend) alignment.

ICASDataSet is a subclass of RangedSummarizedExperiment, used to store the input values, intermediate calculations and results of an analysis of differential expression. The ICASDataSet class enforces non-negative integer values in the "counts" matrix stored as the first element in the assay list. In addition, a formula which specifies the design of the experiment must be provided. The constructor functions create a ICASDataSet object from various types of input: a RangedSummarizedExperiment, a matrix of splice junctions count, or a list of STAR output splice junction files.

Usage

ICASDataSet(se, design)

ICASDataSetFromMatrix(countData, colData, design, ...)

ICASDataSetFromSJFile(SJFiles, postfix = "SJ.out.tab",
  uniqMapOnly = TRUE, annotationOnly = FALSE, minSJRead = 2,
  minOverhang = 3, minSJRowSum = 100, colData, design, ...)

Arguments

se	a RangedSummarizedExperiment with columns of variables indicating sample information in colData, and the counts as the first element in the assays list, which will be renamed "counts". A RangedSummarizedExperiment object can be generated by the function summarizeOverlaps in the GenomicAlignments package.
design	a character. the character indicate how to group the counts for each gene depend on the variables in colData.
countData	for matrix input: a matrix of non-negative integers
colData	for matrix input: a DataFrame or data.frame with at least a single column. Rows of colData correspond to columns of countData
...	arguments provided to SummarizedExperiment including rowRanges and metadata. Note that for Bioconductor 3.1, rowRanges must be a GRanges or GRangesList, with potential metadata columns as a DataFrame accessed and stored with mcols. If a user wants to store metadata columns about the rows of the countData, but does not have GRanges or GRangesList information, first construct the ICASDataSet without rowRanges and then add the DataFrame with mcols(dds).
SJFiles	A character vector containing the names of the STAR outputed **SJ.out.tab** files in the specified directories.
postfix	The postfix of STAR outputed **SJ.out.tab**, [default is SJ.out.tab]
uniqMapOnly	a logical value indicating whether only the uniquely mapping reads crossing the junction to be used
annotationOnly	a logical value indicating whether only the annotated reads crossing the junction to be used
minSJRead	the minimum number of reads crossing each junction of each sample
minOverhang	the minimum length of maximum spliced alignment overhang of each junction of each sample
minSJRowSum	the minimum number of reads crossing each junction of all samples

Details

See the vignette for examples of construction from different types.

Value

A ICASDataSet object.

Slots

counts

The raw SJ counts are stored in RangedSummarizedExperiment Container.

psi

The PSI of same start of all SJs are stored in RangedSummarizedExperiment Container.

rowRanges

The GRanges format information of all SJs are stored in RangedSummarizedExperiment Container.

colData

The sample information are stored in RangedSummarizedExperiment Container.

design

A formula about your experimental design.

HostGene

The host gene of all SJs. For novel (unannotated in GTF) SJs we use range overlap method and we give all the covered genes and the genes anchored by the cleavage site at the same time.

ASType

The AS type of each ASSJ

References

See https://github.com/alexdobin/STAR for STAR

Examples

countData <- matrix(1:100,ncol=4)
condition <- factor(c("A","A","B","B"))
dds <- ICASDataSetFromMatrix(countData, DataFrame(condition), condition)

tangchao7498/ICAS documentation built on Jan. 28, 2021, 3:56 p.m.