qcrlscR (version 0.1.3)

mv.filter.qc: Data filtering based on "qc" missing values

Description

Data filtering based on "qc" missing values

Usage

mv.filter.qc(x, y, thres = 0.3)

Value

a list of with contents:

• dat the filtered data matrix

• idx a logical vector of index for keeping features.

Arguments

x

a data matrix.

y

a character string with contents of "sample", "qc" and "blank".

thres

threshold of missing values. Features less than this threshold will be kept.

See Also

Other missing value processing: mv.filter(), mv.perc()

Examples

names(man_qc)
data <- man_qc$data
meta <- man_qc$meta
## check missing value rates
tail(sort(mv.perc(data)), 20)
## missing values filtering based on QC
cls.qc <- factor(meta$sample_type)
tmp <- mv.filter.qc(data, cls.qc, thres = 0.15)
data_f <- tmp$dat
## compare
dim(data_f)
dim(data)