handleNA: Deal with NAs in the dataset!

In kkdey/CountClust: Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models

Description

This function handles the NA values in the count data. If for a feature, the proportion of NAs is greater than threshold proportion, then we remove the feature, otherwise we use MAR substitution scheme using the distribution of the non NA values for the feature. If threshold proportion is 0, it implies removal of all features with NA values. Default value of threshold proportion is 0.

Usage

handleNA(data, thresh_prop = 0)

Arguments

data	count data in a sample by feature matrix.
thresh_prop	threshold proportion of NAs for removal of feature or replacing the NA values.

Details

This function removes NAs from the counts data

Value

Returns a list with

data	The modified data with NA substitution and removal
na_removed_cols	The columns in the data with NAs that were removed
na_sub_cols	The columns in the data with NAs that were substituted

Examples

mat <- rbind(c(2,4,NA),c(4,7,8),c(3,NA,NA));
handleNA(mat,thresh_prop=0.5)
handleNA(mat)

kkdey/CountClust documentation built on Jan. 17, 2021, 5:32 p.m.