Undefined methods

Description

These are methods defined for GRanges and GRangesList objects that have no well-defined equivalent for GTuples or GTuplesList. Therefore, I have explicitly written methods for these that return errors when called.

Examples

  gt3 <- GTuples(seqnames = c('chr1', 'chr1', 'chr1', 'chr1', 'chr2'), 
                 tuples = matrix(c(10L, 10L, 10L, 10L, 10L, 20L, 20L, 20L, 25L, 
                                   20L, 30L, 30L, 35L, 30L, 30L), ncol = 3), 
                 strand = c('+', '-', '*', '+', '+'))
  ## Not run: 
  # Will return errors
  narrow(gt3)
  reduce(gt3)
  
## End(Not run)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(GenomicTuples)
Loading required package: GenomicRanges
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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GenomicTuples/illdefined-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Undefined methods
> ### Title: Undefined methods
> ### Aliases: replaceROWS,NULL-method coverage,GTuples-method
> ###   coverage,GTuplesList-method flank,GTuples-method
> ###   flank,GTuplesList-method promoters,GTuples-method
> ###   promoters,GTuplesList-method resize,GTuples-method
> ###   resize,GTuplesList-method restrict,GTuplesList-method narrow
> ###   narrow,GTuples-method disjoin,GTuples-method
> ###   disjoin,GTuplesList-method disjointBins,GTuples-method
> ###   gaps,GTuples-method isDisjoint,GTuples-method
> ###   isDisjoint,GTuplesList-method range,GTuples-method
> ###   range,GTuplesList-method reduce,GTuples-method
> ###   reduce,GTuplesList-method Ops,GTuples,numeric-method
> ###   intersect,GTuples,GTuples-method pgap,GTuples,GTuples-method
> ###   pintersect,GTuples,GTuples-method
> ###   pintersect,GTuples,GTuplesList-method
> ###   pintersect,GTuplesList,GTuples-method
> ###   pintersect,GTuplesList,GTuplesList-method
> ###   psetdiff,GTuples,GTuples-method psetdiff,GTuples,GTuplesList-method
> ###   psetdiff,GTuplesList,GTuplesList-method punion,GTuples,GTuples-method
> ###   punion,GTuples,GTuplesList-method punion,GTuplesList,GTuples-method
> ###   setdiff,GTuples,GTuples-method union,GTuples,GTuples-method
> ###   tile,GTuples-method
> 
> ### ** Examples
> 
>   gt3 <- GTuples(seqnames = c('chr1', 'chr1', 'chr1', 'chr1', 'chr2'), 
+                  tuples = matrix(c(10L, 10L, 10L, 10L, 10L, 20L, 20L, 20L, 25L, 
+                                    20L, 30L, 30L, 35L, 30L, 30L), ncol = 3), 
+                  strand = c('+', '-', '*', '+', '+'))
>   ## Not run: 
> ##D   # Will return errors
> ##D   narrow(gt3)
> ##D   reduce(gt3)
> ##D   
> ## End(Not run)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>