presenceFilt {wrMisc}

Filter lines of matrix for max number of NAs

Description

This function produces a logical matrix to be used as filter for lines of 'dat' for sufficient presence of non-NA values (ie limit number of NAs per line). Filter abundance/expression data for min number and/or ratio of non-NA values in at east 1 of multiple groups. This type of procedure is common in proteomics and tanscriptomics, where a NA can many times be assocoaued with quantitation below detetction limit.

Usage

presenceFilt(
  dat,
  grp,
  maxGrpMiss = 1,
  ratMaxNA = 0.8,
  minVal = NULL,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

dat

matrix or data.frame (abundance or expression-values which may contain some NAs).

grp

factor of min 2 levels describing which column of 'dat' belongs to which group (levels 1 & 2 will be used)

maxGrpMiss

(numeric) at least 1 group has not more than this number of NAs (otherwise marke line as bad)

ratMaxNA

(numeric) at least 1 group reaches this content of non-NA values

minVal

(default NULL or numeric), any value below will be treated like NA

silent

(logical) suppress messages

debug

(logical) additional messages for debugging

callFrom

(character) allow easier tracking of messages produced

Value

logical matrix (with separate col for each pairwise combination of 'grp' levels) indicating if line of 'dat' acceptable based on NAs (and values minVal)

See Also

presenceGrpFilt, there are also other packages totaly dedicated to filtering on CRAN and Bioconductor

Examples

mat <- matrix(rep(8,150), ncol=15, dimnames=list(NULL,
  paste0(rep(LETTERS[4:2],each=6),1:6)[c(1:5,7:16)]))
mat[lower.tri(mat)] <- NA
mat[,15] <- NA
mat[c(2:3,9),14:15] <- NA
mat[c(1,10),13:15] <- NA
mat
presenceFilt(mat ,rep(LETTERS[4:2], c(5,6,4)))
presenceFilt(mat, rep(1:2,c(9,6)))

# one more example 
dat1 <- matrix(1:56, ncol=7)
dat1[c(2,3,4,5,6,10,12,18,19,20,22,23,26,27,28,30,31,34,38,39,50,54)] <- NA
dat1; presenceFilt(dat1,gr=gl(3,3)[-(3:4)], maxGr=0)
presenceFilt(dat1, gr=gl(2,4)[-1], maxGr=1, ratM=0.1)
presenceFilt(dat1, gr=gl(2,4)[-1], maxGr=2, rat=0.5)