mdsChr22IntSpObj: Object of SummarizedExperiment type for intron spanning reads...

In gacatag/IntEREst: Intron-Exon Retention Estimator

Object of SummarizedExperiment type for intron spanning reads of MDS data

Description

The Results of interest() analysis in intron-spanning mode, for the genes that feature U12-type introns and are located on Chr22 in MDS data.

Usage

data(mdsChr22ExObj)

Format

An Object of class SummarizedExperiment that contains intron retention results generated by interest() function on MDS data consisting of bone-marrows samples of 8 MDS patients with ZRSR2 mutations, 4 patients without the mutation and 4 healthy individuals.

@colData

A "DataFrame" (from "S4Vectors" package) that its rownames can be set as the sample identification names and the other columns are various annotations for the samples. Its column names are characters that describe the annotations.

@assays

List of size 2 that includes two numeric matrices: counts that includes raw read counts of the sequencing reads mapped to introns and exons, and (2) scaledRetention, i.e. the normalized read counts.

@NAMES

A NULL value.

@elementMetadata

A "DataFrame" (from "S4Vectors" package) that include intron and exon annotations.

@metadata

A list of size 2 that includes parameter settings for the interest() and interest.sequential() runs.

Value

Object of class SummarizedExperiment.

Source

Madan, V., et.al., Aberrant splicing of U12-type introns is the hallmark of ZRSR2 mutant myelodysplastic syndrome. Nat Communication 2015 Jan 14;6:6042. doi: 10.1038/ncomms7042.

gacatag/IntEREst documentation built on July 29, 2024, 1:12 a.m.