normalize-methods: description of function normalize

Description Usage Arguments Value

Description

normalize the expression data (sample wise)

normalize the expression data by subsampling as described in PMID 24531970

Usage

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normalize(object, ..., reads = 600, name = "normalized")

normalize(object, ..., reads = 600, name = "normalized")

Arguments

reads

the required read depth

name

the name of the new object

x

The NGSexpressionSet

readCounts

The number of reads from each bam file or another value you want to normalize the data to

to_gene_length

FALSE whether or not to normalize the data to gene length

geneLengthCol

the column in the annotation data.frame to (in addition) normalize the genes to (e.g. trancript length)

x

The SingleCellsNGS object

Value

the normalized data set (original data stored in NGS$raw

the normalized data set (original data stored in slot 'raw'


stela2502/NGSexpressionSet documentation built on May 30, 2019, 2:36 p.m.