mcwBestCis instances, integrative analysis output containers generated by GGtools vignette

Description

integrative analysis output containers generated by GGtools vignette

Usage

data(b1)

Format

The format is:
Formal class 'mcwBestCis' [package "GGtools"] with 9 slots
..@ scoregr :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots
.. .. ..@ seqnames :Formal class 'Rle' [package "IRanges"] with 4 slots
.. .. .. .. ..@ values : Factor w/ 1 level "20": 1
.. .. .. .. ..@ lengths : int 50
.. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. ..@ metadata : list()
.. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots
.. .. .. .. ..@ start : int [1:50] 24280834 61665697 352356 61679079 45286150 55187941 38766161 10871477 56570242 13304639 ...
.. .. .. .. ..@ width : int [1:50] 2090785 2005619 2021461 2001901 2129211 2007692 2038197 2035767 2012068 2013675 ...
.. .. .. .. ..@ NAMES : chr [1:50] "GI_34147330-S" "hmm26961-S" "GI_17149835-I" "GI_31077201-S" ...
.. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. ..@ metadata : list()
.. .. ..@ strand :Formal class 'Rle' [package "IRanges"] with 4 slots
.. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 3
.. .. .. .. ..@ lengths : int 50
.. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. ..@ metadata : list()
.. .. ..@ elementMetadata:Formal class 'DataFrame' [package "IRanges"] with 6 slots
.. .. .. .. ..@ rownames : NULL
.. .. .. .. ..@ nrows : int 50
.. .. .. .. ..@ listData :List of 6
.. .. .. .. .. ..$ score : num [1:50] 36.5 16.8 16.7 14.8 9.8 ...
.. .. .. .. .. ..$ snpid : chr [1:50] "rs6037097" "rs3810504" "rs13043344" "rs13044229" ...
.. .. .. .. .. ..$ snploc : int [1:50] 25347221 62678549 544417 61738288 46369894 56551001 38879237 12177765 57565943 15056960 ...
.. .. .. .. .. ..$ radiusUsed: num [1:50] 1e+06 1e+06 1e+06 1e+06 1e+06 1e+06 1e+06 1e+06 1e+06 1e+06 ...
.. .. .. .. .. ..$ nsnp : int [1:50] 1387 783 2382 766 2157 2238 1658 2459 1675 1868 ...
.. .. .. .. .. ..$ fdr : num [1:50] 0 0 0 0.25 0.717 ...
.. .. .. .. ..@ elementType : chr "ANY"
.. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. ..@ metadata : list()
.. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomicRanges"] with 4 slots
.. .. .. .. ..@ seqnames : chr "20"
.. .. .. .. ..@ seqlengths : int NA
.. .. .. .. ..@ is_circular: logi NA
.. .. .. .. ..@ genome : chr NA
.. .. ..@ metadata : list()
..@ allperm : num [1:100] 15.8 13.9 13.8 13.2 13 ...
..@ extra : NULL
..@ chromUsed: chr "20"
..@ theCall : language best.cis.eQTLs(smpack = "GGdata", rhs = ~male, folderstem = "db2", radius = 1e+06, chrnames = "20", geneApply = mclapply, snpannopk = snplocsDefault(), ...
..@ smFilter :function (x)
.. ..- attr(*, "srcref")=Class 'srcref' atomic [1:8] 413 8 413 50 8 50 4 4
.. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0xf5c0cc0>
..@ nperm : num 2
..@ globalMap:<environment: 0xf5c0538>
..@ testCount: int 83969

Details

As created in GGtools.Rnw vignette code, with sharply curtailed searches

Examples

data(b1)
b1

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(GGtools)
Loading required package: GGBase
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
Loading required package: data.table
Loading required package: parallel
Loading required package: Homo.sapiens
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

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

Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand, rowMeans, rowSums

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

    colMeans, colSums, expand.grid, rowMeans, rowSums


Attaching package: 'IRanges'

The following object is masked from 'package:data.table':

    shift

Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GO.db

Loading required package: org.Hs.eg.db

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene

Attaching package: 'GGtools'

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

    getCall

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GGtools/b1.Rd_%03d_medium.png", width=480, height=480)
> ### Name: b1
> ### Title: mcwBestCis instances, integrative analysis output containers
> ###   generated by GGtools vignette
> ### Aliases: b1 b2
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(b1)
> b1
GGtools mcwBestCis instance.  The call was:
best.cis.eQTLs(smpack = "GGdata", rhs = ~male, folderstem = "db2", 
    radius = 1e+06, chrnames = "20", geneApply = mclapply, snpannopk = snplocsDefault(), 
    smFilter = exTx, nperm = 2)
Best loci for 50 probes are recorded.
There were 83969 gene:snp tests.
Top  4 probe:SNP combinations:
GRanges object with 4 ranges and 6 metadata columns:
                seqnames               ranges strand |     score       snpid
                   <Rle>            <IRanges>  <Rle> | <numeric> <character>
  GI_34147330-S       20 [24280834, 26371618]      * |     36.49   rs6037097
     hmm26961-S       20 [61665697, 63671315]      * |     16.78   rs3810504
  GI_17149835-I       20 [  352356,  2373816]      * |     16.67  rs13043344
  GI_31077201-S       20 [61679079, 63680979]      * |     14.78  rs13044229
                   snploc radiusUsed      nsnp       fdr
                <integer>  <numeric> <integer> <numeric>
  GI_34147330-S  25347221      1e+06      1387      0.00
     hmm26961-S  62678549      1e+06       783      0.00
  GI_17149835-I    544417      1e+06      2382      0.00
  GI_31077201-S  61738288      1e+06       766      0.25
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
====
use chromsUsed(), fullreport(), etc. for additional information.
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>