checkForConcordance: checkForConcordance

In quevedor2/CCLid: Compares Cancer Cell Line Genotypes Against Pharmacogenomic Datasets

Description

Checks for concordance between sample in first column of input matrix and the rest of the reference matrix

Usage

checkForConcordance(
  x.mat,
  metric = "euclidean",
  meta.dat = NULL,
  verbose = FALSE,
  return.matrix = FALSE,
  return.pred = TRUE,
  fill.na = TRUE,
  rm.gcsi = TRUE,
  sampleID = "Sample",
  meta.df
)

Arguments

x.mat	Input matrix from compareVcf, or ref.mat
metric	'euclidean', 'jaccard', or 'cor'
meta.dat	Metadata, defaults to meta.df if left NULL (default:NULL)
verbose	Verbose
return.matrix	Return distance matrix (Default: FALSE)
return.pred	Return predicted Match/Nonmatch (Default: TRUE)
fill.na	Fill NA's in the input matrix with median value (Default=TRUE)
rm.gcsi	Remove GNE samples from the input matrix (Default=TRUE)
sampleID	Sample ID (Default='Sample')
meta.df	Cell line metadata, accessible from CCLid::ccl_table

Value

A list containing Distance Matrix and list of Predictions (M/NM)

quevedor2/CCLid documentation built on July 15, 2020, 4:05 a.m.