droptax: Dropping Species with Few abundance and Few Occurrences

In xiangpin/MetaMicrobiome: An R package for meta-analysis and visualization of Microbiome.

Description

Drop species or features from the feature data frame that occur fewer than or equal to a threshold number of occurrences and fewer abundance than to a threshold abundance.

Usage

droptax(taxtab, rmode = FALSE, minocc = 0, minabu = 0)

Arguments

taxtab	dataframe; a dataframe of species (or features), default is (n_sample, n_feature).
rmode	boolean; whether transpose the taxtab, default is False.
minocc	numeric; the threshold number of occurrences to be dropped, if < 1.0, it will be the threshold ratios of occurrences, default is 0.
minabu	numeric: the threshold abundance, if fewer than the threshold will be dropped, default is 0.

Value

a list contained feature dataframe dropped, and the call, arguments.

Author(s)

Shuangbin Xu

Examples

library("MetaMicrobiome")
data <- read.csv(system.file("data", package="MetaMicrobiome", "Baxter_16_crc_genera_group.csv.gz"))
data$Group <- NULL
dim(data)
head(data)
newdat <- droptax(data, rmode=FALSE, minocc=0.2, minabu=0)
dim(newdat)
head(newdat)

xiangpin/MetaMicrobiome documentation built on May 26, 2019, 2:34 a.m.