q.clean: Clean data by eliminating genes with many missing values

In QuESTr: Constructing Quantitative Environment Sensor using Transcriptomes

Clean data by eliminating genes with many missing values

Description

Clean data by eliminating genes with many missing values

Usage

q.clean(x, missing = 0.1, lowest = 10)

Arguments

x	A data matrix (raw: samples, col: genes).
missing	A ratio of missing values in each column allowed to be remained in the data.
lowest	The lowest value recognized in the data (e.g., TPM, FPKM, or raw read counts).

Value

A data matrix (raw: samples, col: qualified genes)

Author(s)

Takahiko Koizumi

Examples

data(Pinus)
train.raw <- Pinus$train
ncol(train.raw)

train <- q.clean(train.raw)
ncol(train)

QuESTr documentation built on March 18, 2022, 5:09 p.m.