Filter lines of matrix for max number of NAs
presenceFilt produces 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.
presenceFilt( dat, grp, maxGrpMiss = 1, ratMaxNA = 0.8, minVal = NULL, silent = FALSE, callFrom = NULL )
dat |
matrix or data.frame (abundance or expression-values which may contain some |
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- |
minVal |
(default NULL or numeric), any value below will be treated like |
silent |
(logical) suppress messages |
callFrom |
(character) allow easier tracking of message produced |
logical matrix (with separate col for each pairwise combination of 'grp' levels) indicating if line of 'dat' acceptable based on NAs (and values minVal)
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 wrMisc::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)
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