extract_features: Extracts biological and technical features for given dataset
In Teichlab/cellity: Quality Control for Single-Cell RNA-seq Data

Description Usage Arguments Details Value Examples

Extracts biological and technical features for given dataset

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

`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

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

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

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)