cpneTrack: CPNE1 SNP track

In rtracklayer: R interface to genome annotation files and the UCSC genome browser

Description

A GRanges object (created by the GGtools package) with features from a subset of the SNPs on chromosome 20 from 60 HapMap founders in the CEU cohort. Each SNP has an associated data value indicating its association with the expression of the CPNE1 gene according to a Cochran-Armitage 1df test. The top 5000 scoring SNPs were selected for the track.

Usage

data(cpneTrack)

Format

Each feature (row) is a SNP. The association test scores are accessible via score.

Source

Vince Carey and the GGtools package.

Examples

data(cpneTrack)
plot(start(cpneTrack), score(cpneTrack))

Example output

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb

rtracklayer documentation built on Nov. 8, 2020, 6:50 p.m.