wrProteo (version 1.13.1)

combineMultFilterNAimput: Combine Multiple Filters On NA-imputed Data

Description

In most omics data-analysis one needs to employ a certain number of filtering strategies to avoid getting artifacts to the step of statistical testing. combineMultFilterNAimput takes on one side the origial data and on the other side NA-imputed data to create several differnet filters and to finally combine them. A filter aiming to take away the least abundant values (using the imputede data) can be fine-tuned by the argument abundThr. This step compares the means for each group and line, at least one grou-mean has to be > the threshold (based on hypothesis that if all conditions represent extrememy low measures their diffrenetial may not be determined with certainty). In contrast, the filter addressing the number of missing values (NA) uses the original data, the arguments colTotNa,minSpeNo and minTotNo are used at this step. Basically, this step allows defining a minimum content of 'real' (ie non-NA) values for further considering the measurements as reliable. This part uses internally presenceFilt for filtering elevated content of NA per line. Finally, this function combines both filters (as matrix of FALSE and TRUE) on NA-imputed and original data and retruns a vector of logical values if corresponding lines passe all filter criteria.

Usage

combineMultFilterNAimput(
  dat,
  imputed,
  grp,
  annDat = NULL,
  abundThr = NULL,
  colRazNa = NULL,
  colTotNa = NULL,
  minSpeNo = 1,
  minTotNo = 2,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Value

This function returns a vector of logical values if corresponding line passes filter criteria

Arguments

dat

(matrix or data.frame) main data (may contain NA)

imputed

(character) same as 'dat' but with all NA imputed

grp

(character or factor) define groups of replicates (in columns of 'dat')

annDat

(matrix or data.frame) annotation data (should match lines of 'dat')

abundThr

(numeric) optional threshold filter for minimumn abundance

colRazNa

(character) if razor peptides are used: column name for razor peptide count

colTotNa

(character) column name for total peptide count

minSpeNo

(integer) minimum number of specific peptides for maintaining proteins

minTotNo

(integer) minimum total ie max razor number of peptides

silent

(logical) suppress messages

debug

(logical) additional messages for debugging

callFrom

(character) allows easier tracking of messages produced

See Also

presenceFilt

Examples

set.seed(2013)
datT6 <- matrix(round(rnorm(300)+3,1), ncol=6,
  dimnames=list(paste0("li",1:50), letters[19:24]))
datT6 <- datT6 +matrix(rep(1:nrow(datT6),ncol(datT6)), ncol=ncol(datT6))
datT6[6:7,c(1,3,6)] <- NA
datT6[which(datT6 < 11 & datT6 > 10.5)] <- NA
datT6[which(datT6 < 6 & datT6 > 5)] <- NA
datT6[which(datT6 < 4.6 & datT6 > 4)] <- NA
datT6b <- matrixNAneighbourImpute(datT6, gr=gl(2,3))
datT6c <- combineMultFilterNAimput(datT6, datT6b, grp=gl(2,3), abundThr=2)