phy_drop_NA_vars: Drop NAs from selected variables

In g-antonello/gautils2: Wrapper of my functions to wrangle mostly microbiome data

Drop NAs from selected variables

Description

Given a phyloseq object and a character vector, the function removes all NAs that are in at least one variable

Usage

phy_drop_NA_vars(physeq, variables, verbose = TRUE)

Arguments

physeq	a phyloseq object
variables	a character vector with variable names to remove NAs from
verbose	A logical. If TRUE, it will print how many samples per variable it removed

Value

a clean phyloseq object

Examples

data("GlobalPatterns")
set.seed(1111)
GlobalPatternsNA <- GlobalPatterns
GlobalPatternsNA@sam_data$newVar1 <- replicate(n = nsamples(GlobalPatternsNA), expr = sample(x =c(NA, 1,0), size = 1, prob = c(0.1, 0.4, 0.5)))
GlobalPatternsNA@sam_data$newVar2 <- replicate(n = nsamples(GlobalPatternsNA), expr = sample(x =c(NA, 1,0), size = 1, prob = c(0.1, 0.4, 0.5)))

drop_NA_from_phyloseq_vars(physeq = GlobalPatternsNA, vars = c("newVar1", "newVar2"))
GlobalPatterns

g-antonello/gautils2 documentation built on Nov. 28, 2022, 9:39 a.m.