Y chromosome probe list

Description

A list containing probes corresponding to y chromosome genes for Illumina and Affymetrix platforms. Each item in the list is a data.frame of y chromosome probes that can be used in the massi analysis. The names of each item in the list correspond to the ensembl biomart attribute names.

Usage

data(y.probes)

Format

The format is: List of 6 $ illumina_humanwg_6_v1:'data.frame': 58 obs. of 0 variables $ illumina_humanwg_6_v2:'data.frame': 74 obs. of 0 variables $ illumina_humanwg_6_v1:'data.frame': 112 obs. of 0 variables $ illumina_humanht_12 :'data.frame': 112 obs. of 0 variables $ affy_hugene_1_0_st_v1:'data.frame': 138 obs. of 0 variables $ affy_hg_u133_plus_2 :'data.frame': 94 obs. of 0 variables

Details

The y chromosome probes for each platform were downloaded from Ensembl biomart using the 'biomaRt' package. For more details on the methods of selecting the probes and how to obtain probes for other platform, see the vignette for the massiR package.

References

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Steffen Durinck, Paul T. Spellman, Ewan Birney and Wolfgang Huber, Nature Protocols 4, 1184-1191 (2009).

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Steffen Durinck, Yves Moreau, Arek Kasprzyk, Sean Davis, Bart De Moor, Alvis Brazma and Wolfgang Huber, Bioinformatics 21, 3439-3440 (2005).

Examples

# load the probes list
data(y.probes)
# look at the platform names
names(y.probes)
# extract the probes using the platform name
probe.list <- y.probes[["illumina_humanwg_6_v2"]]

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(massiR)
Loading required package: cluster
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

Loading required package: diptest
Loading required package: Biobase
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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/massiR/y_probes.Rd_%03d_medium.png", width=480, height=480)
> ### Name: y.probes
> ### Title: Y chromosome probe list
> ### Aliases: y.probes
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> # load the probes list
> data(y.probes)
> # look at the platform names
> names(y.probes)
[1] "illumina_humanwg_6_v1" "illumina_humanwg_6_v2" "illumina_humanwg_6_v1"
[4] "illumina_humanht_12"   "affy_hugene_1_0_st_v1" "affy_hg_u133_plus_2"  
> # extract the probes using the platform name
> probe.list <- y.probes[["illumina_humanwg_6_v2"]]
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>