nni: Nearest neighbour imputation

In pcaMethods: A collection of PCA methods

Description

Wrapper function for imputation methods based on nearest neighbour clustering. Currently llsImpute only.

Usage

nni(object, method = c("llsImpute"), subset = numeric(), ...)

Arguments

object	Numerical matrix with (or an object coercible to such) with samples in rows and variables as columns. Also takes ExpressionSet in which case the transposed expression matrix is used.
method	For convenience one can pass a large matrix but only use the variable specified as subset. Can be colnames or indices.
subset	Currently "llsImpute" only.
...	Further arguments to the chosen method.

Details

This method is wrapper function to llsImpute, See documentation for link{llsImpute}.

Value

A clusterRes object. Or a list containing a clusterRes object as first and an ExpressionSet object as second entry if the input was of type ExpressionSet.

Author(s)

Wolfram Stacklies

See Also

llsImpute, pca

Examples

data(metaboliteData)
llsRes <- nni(metaboliteData, k=6, method="llsImpute", allGenes=TRUE)

Example output

Loading required package: Biobase
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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

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


Attaching package: 'pcaMethods'

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

    loadings

Warning message:
In llsImpute(object, ...) :
  Cluster size larger than number of complete genes, using allVariables = TRUE

pcaMethods documentation built on Nov. 8, 2020, 6:19 p.m.