wrProteo: isolNAneighb – R documentation

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isolNAneighb

Isolate NA-neighbours

Description

This functions extracts all replicate-values where at least one of the replicates is NA. Then, the non-NA values are sorted by the number of NAs which occored in this group of replicates. A list with all NA-neighbours organized by the number of NAs gets returned.

Usage

isolNAneighb(mat, gr, maxHi = 3, iniCheck = TRUE, callFrom = NULL)

Arguments

`mat`	(matrix or data.frame) main data (may contain `NA`)
`gr`	(character or factor) grouping of columns of 'mat', replicate association
`maxHi`	(integer) maximum count of NAs to consider separately (higher ones will be counted/pooled as maxHi)
`iniCheck`	(logical) check at beginning if executing this function is useful (presence any `NA`)
`callFrom`	(character) allow easier tracking of message(s) produced

Value

list with NA-neighbours sorted by number of NAs in replicate group

Examples

mat1 <- c(22.2, 22.5, 22.2, 22.2, 21.5, 22.0, 22.1, 21.7, 21.5, 22, 22.2, 22.7,
  NA, NA, NA, NA, NA, NA, NA, 21.2,   NA, NA, NA, NA,
  NA, 22.6, 23.2, 23.2,  22.4, 22.8, 22.8, NA,  23.3, 23.2, NA, 23.7,
  NA, 23.0, 23.1, 23.0,  23.2, 23.2, NA, 23.3,  NA, NA, 23.3, 23.8)
mat1 <- matrix(mat1, ncol=12, byrow=TRUE)
gr4 <- gl(3, 4)
isolNAneighb(mat1, gr4)

wrProteo

Proteomics Data Analysis Functions

v1.4.1

GPL-3

Authors

Wolfgang Raffelsberger [aut, cre]

Initial release