q.clean {QuESTr}

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)