Normalize each column of the input matrix by the column sum

Normalize each column of the input matrix by the column sum

Usage

colNormalize(x, scaleFactor = NULL, log = FALSE, ...)

# S3 method for default
colNormalize(x, scaleFactor = NULL, log = FALSE, ...)

# S3 method for dgCMatrix
colNormalize(x, scaleFactor = NULL, log = FALSE, ...)

# S3 method for Seurat
colNormalize(
  x,
  scaleFactor = NULL,
  log = FALSE,
  assay = NULL,
  layer = "counts",
  ...
)

# S3 method for SingleCellExperiment
colNormalize(x, scaleFactor = NULL, log = FALSE, assay.type = "counts", ...)

Arguments

x

Feature by observation matrix. Alternatively, Seurat object or SingleCellExperiment object with raw counts available are also supported.

scaleFactor

Multiplier on normalized data. Default NULL.

log

Logical. Whether to take log1p transformation after scaling. Default FALSE

...

Additional arguments passed to methods

assay

For "Seurat" method, the specific assay to get data from. Default NULL to the default assay.

layer

For "Seurat" method, which layer of the assay to be used. Default "counts".

assay.type

For "SingleCellExperiment" method, the assay type to get data from. Default "counts".

Value

Normalized matrix of the same size

A Seurat object with normalized data in the specified slot of the specified assay.

A SingleCellExperiment object with normalized data in the specified assay. "normcounts" if log = FALSE and "logcounts" if log = TRUE.

Examples

rnaNorm <- colNormalize(rnaRaw)
# \donttest{
# Seurat example
library(Seurat)
#> Loading required package: SeuratObject
#> Loading required package: sp
#> 
#> Attaching package: ‘SeuratObject’
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, t
srt <- CreateSeuratObject(rnaRaw)
#> Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-')
srt <- colNormalize(srt)
# }
# \donttest{
# SingleCellExperiment example
library(SingleCellExperiment)
#> Loading required package: 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 object is masked from ‘package:SeuratObject’:
#> 
#>     intersect
#> 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, 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
#> 
#> Attaching package: ‘IRanges’
#> The following object is masked from ‘package:sp’:
#> 
#>     %over%
#> 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
#> 
#> Attaching package: ‘SummarizedExperiment’
#> The following object is masked from ‘package:Seurat’:
#> 
#>     Assays
#> The following object is masked from ‘package:SeuratObject’:
#> 
#>     Assays
sce <- SingleCellExperiment(assays = list(counts = rnaRaw))
sce <- colNormalize(sce)
# }