Alu.hg38.demo: Subset of Alu genomic location dataset (hg38)

In YinanZheng/REMP: Repetitive Element Methylation Prediction

Subset of Alu genomic location dataset (hg38)

Description

A GRanges dataset containing 500 Alu sequences that have CpGs profiled by both Illumina 450k and EPIC array. The variables are as follows:

Usage

Alu.hg38.demo

Format

A GRanges object.

Details

• seqnames: chromosome number

• ranges: hg38 genomic position

• strand: DNA strand

• swScore: Smith Waterman (SW) alignment score

• repName: Alu name

• repClass: Alu class

• repFamily: Alu family

• Index: internal index (meaningless for external use; not communicable between genome builds)

Alu.hg38.demo has the same format as the data object returned by fetchRMSK.

Value

A GRanges object with 500 ranges and 3 metadata columns.

Source

RepeatMasker database (hg38) is provided by UCSC database downloaded from http://hgdownload.cse.ucsc.edu/goldenpath.

See Also

See fetchRMSK to obtain the complete Alu/L1 dataset.

YinanZheng/REMP documentation built on May 14, 2022, 5:58 p.m.