cellity (version 1.0.2)

extract_features: Extracts biological and technical features for given dataset

Description

Extracts biological and technical features for given dataset

Usage

extract_features(counts_nm, read_metrics, prefix = "", output_dir = "", common_features = NULL, GO_terms = NULL, extra_genes = NULL, organism = "mouse")

Arguments

counts_nm

Gene expression counts dataframe (genes x cells). Either normalised by library size or TPM values

read_metrics

Dataframe with mapping statistics produced by python pipeline

prefix

Prefix of outputfiles

output_dir

Output directory of files

common_features

Subset of features that are applicable within one species, but across cell types

GO_terms

DataFrame with gene ontology term IDs, that will be used in feature extraction

extra_genes

Additional genes used for feature extraction

organism

The target organism to generate the features for

Value

a list with two elements, one providing all features, and one providing common features.

Details

This function takes a combination of gene counts and mapping statistics to extract biological and technical features, which than can be used for quality data analysis

Examples

data(sample_counts)
data(sample_stats)
sample_counts_nm <- normalise_by_factor(sample_counts, colSums(sample_counts))
sample_features <- extract_features(sample_counts_nm, sample_stats)