getSlopes {SCnorm} | R Documentation

## Estimate gene specific count-depth relationships

### Description

This is the gene-specific fitting function, where a median (Tau = .5) quantile regression is fit for each gene. Only genes having at least 10 non-zero expression values are considered.

### Usage

    getSlopes(
      Data,
      SeqDepth = 0,
      Tau = 0.5,
      FilterCellNum = 10,
      ditherCounts = FALSE
    )

### Arguments

`Data` | matrix of un-normalized expression counts. Rows are genes and columns are samples.
`SeqDepth` | vector of sequencing depths estimated as columns sums of un-normalized expression matrix.
`Tau` | value of quantile for the quantile regression used to estimate gene-specific slopes (default is median, Tau = .5 ).
`FilterCellNum` | the number of non-zero expression estimate required to include the genes into the SCnorm fitting (default = 10). The initial
`ditherCounts` | whether to dither/jitter the counts, may be used for data with many ties, default is FALSE.

### Value

vector of estimated slopes.

### Author(s)

Rhonda Bacher

### Examples

     data(ExampleSimSCData)
     myslopes <- getSlopes(ExampleSimSCData)

[Package SCnorm version 1.12.1 Index]