combineByEitherFactor: Create factor-like column regrouping data regrouping...

In wrMisc: Analyze Experimental High-Throughput (Omics) Data

Create factor-like column regrouping data regrouping simultaneaously by two factors

Description

This function aims to address the situation when two somehow different groupins (of the same data) exist and need to be joined. It is not necessary that both alternative groupings use the same labels, neither. combineByEitherFactor adds new (last) column named 'grp' to input matrix representing the combined factor relative to 2 specified columns from input matrix mat (via 'refC1','refC2'). Optionally, the output may be sorted and a column giving n per factor-level may be added. The function treats selected columns of mat as pairwise combination of 2 elements (that may occur multiple times over all lines of mat) and sorts/organizes all instances of such combined elements (ie from both selected columns) as repeats of a given group, who's class number is given in output column 'grp', the (total) number of repeats may be displayed in column 'nGrp' ( nByGrp=TRUE). If groups are overlapping (after re-ordering), an iterative process of max 3x2 passes will be launched after initial matching. Works on numeric as well as character input.

Usage

combineByEitherFactor(
  mat,
  refC1,
  refC2,
  nByGrp = FALSE,
  convergeMax = TRUE,
  callFrom = NULL,
  debug = FALSE,
  silent = FALSE
)

Arguments

mat	main input matrix
refC1	(integer) column-number of 'mat' to use as 1st set
refC2	(integer) column-number of 'mat' to use as 2nd set
nByGrp	(logical) add last col with n by group
convergeMax	(logical) if TRUE, run 2 add'l iteartive steps to search convergence to stable result
callFrom	(character) allow easier tracking of message(s) produced
debug	(logical) display additional messages for debugging
silent	(logical) suppress messages

Value

This function returns a matrix containing both selected columns plus additional column(s) indicating group-number of the pair-wise combination (and optional the total n by group)

Examples

nn <- rep(c("a","e","b","c","d","g","f"),c(3,1,2,2,1,2,1))
qq <- rep(c("m","n","p","o","q"),c(2,1,1,4,4))
nq <- cbind(nn,qq)[c(4,2,9,11,6,10,7,3,5,1,12,8),]
combineByEitherFactor(nq,1,2,nBy=TRUE); combineByEitherFactor(nq,1,2,nBy=FALSE)
combineByEitherFactor(nq,1,2,conv=FALSE); combineByEitherFactor(nq,1,2,conv=TRUE)
##
mm <- rep(c("a","b","c","d","e"),c(3,4,2,3,1)); pp <- rep(c("m","n","o","p","q"),c(2,2,2,2,5))
combineByEitherFactor(cbind(mm,pp), 1, 2, con=FALSE, nBy=TRUE)
combineByEitherFactor(cbind(mm,pp), 1, 2, con=TRUE, nBy=TRUE) 

wrMisc documentation built on May 29, 2024, 5:44 a.m.