Get or set feature group definitions from an object
Source:R/AllGenerics.R, R/featureGroups.R
featureGroups.RdfeatureGroups and featureGroups<- allow to extract or set the feature
definitions from the input object. The implementations for
SummarizedExperiment() get or set the content of a column named
"feature_group" in the object's rowData.
This method should be implemented for all other object for which a
groupFeatures() method is defined.
Usage
featureGroups(object, ...)
featureGroups(object) <- value
# S4 method for SummarizedExperiment
featureGroups(object)
# S4 method for SummarizedExperiment
featureGroups(object) <- valueArguments
- object
the input object. In the
MsFeaturespackage this method is implemented forSummarizedExperiment.- ...
ignored.
- value
the new value for the feature groups variable.
Value
a character with the group assignment of the features. Has to have
the same length as there are features in object.
Examples
## Load the test SummarizedExperiment
library(SummarizedExperiment)
#> Loading required package: MatrixGenerics
#> Loading required package: matrixStats
#>
#> Attaching package: ‘MatrixGenerics’
#> The following objects are masked from ‘package:matrixStats’:
#>
#> colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
#> colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
#> colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
#> colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
#> colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
#> colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
#> colWeightedMeans, colWeightedMedians, colWeightedSds,
#> colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
#> rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
#> rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
#> rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
#> rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
#> rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
#> rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
#> rowWeightedSds, rowWeightedVars
#> Loading required package: GenomicRanges
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#>
#> Attaching package: ‘BiocGenerics’
#> 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, aperm, append,
#> as.data.frame, basename, cbind, colnames, dirname, do.call,
#> duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
#> lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
#> pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
#> tapply, union, unique, unsplit, which.max, which.min
#> Loading required package: S4Vectors
#>
#> Attaching package: ‘S4Vectors’
#> The following object is masked from ‘package:utils’:
#>
#> findMatches
#> The following objects are masked from ‘package:base’:
#>
#> I, expand.grid, unname
#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
#> 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")'.
#>
#> Attaching package: ‘Biobase’
#> The following object is masked from ‘package:MatrixGenerics’:
#>
#> rowMedians
#> The following objects are masked from ‘package:matrixStats’:
#>
#> anyMissing, rowMedians
data(se)
## No column "feature_group" present in the object, this NA is returned
featureGroups(se)
#> [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [101] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [126] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [151] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [176] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
#> [201] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
## Add a column "feature_group" to the `rowData` of the object
rowData(se)$feature_group <- seq_len(nrow(rowData(se)))
featureGroups(se)
#> [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12"
#> [13] "13" "14" "15" "16" "17" "18" "19" "20" "21" "22" "23" "24"
#> [25] "25" "26" "27" "28" "29" "30" "31" "32" "33" "34" "35" "36"
#> [37] "37" "38" "39" "40" "41" "42" "43" "44" "45" "46" "47" "48"
#> [49] "49" "50" "51" "52" "53" "54" "55" "56" "57" "58" "59" "60"
#> [61] "61" "62" "63" "64" "65" "66" "67" "68" "69" "70" "71" "72"
#> [73] "73" "74" "75" "76" "77" "78" "79" "80" "81" "82" "83" "84"
#> [85] "85" "86" "87" "88" "89" "90" "91" "92" "93" "94" "95" "96"
#> [97] "97" "98" "99" "100" "101" "102" "103" "104" "105" "106" "107" "108"
#> [109] "109" "110" "111" "112" "113" "114" "115" "116" "117" "118" "119" "120"
#> [121] "121" "122" "123" "124" "125" "126" "127" "128" "129" "130" "131" "132"
#> [133] "133" "134" "135" "136" "137" "138" "139" "140" "141" "142" "143" "144"
#> [145] "145" "146" "147" "148" "149" "150" "151" "152" "153" "154" "155" "156"
#> [157] "157" "158" "159" "160" "161" "162" "163" "164" "165" "166" "167" "168"
#> [169] "169" "170" "171" "172" "173" "174" "175" "176" "177" "178" "179" "180"
#> [181] "181" "182" "183" "184" "185" "186" "187" "188" "189" "190" "191" "192"
#> [193] "193" "194" "195" "196" "197" "198" "199" "200" "201" "202" "203" "204"
#> [205] "205" "206" "207" "208" "209" "210" "211" "212" "213" "214" "215" "216"
#> [217] "217" "218" "219" "220" "221" "222" "223" "224" "225"