b1: mcwBestCis instances, integrative analysis output containers...
In GGtools: software and data for analyses in genetics of gene expression

Description Usage Format Details Examples

integrative analysis output containers generated by GGtools vignette

data(b1)

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