denoise: Denoise data by setting all latent factors to their median...

Description Usage Arguments Value Examples

View source: R/denoise.R

Description

Denoise data by setting all latent factors to their median values and reversing the regression model

Usage

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denoise(x, data = "y", cell_attr = x$cell_attr, do_round = TRUE,
  do_pos = TRUE, show_progress = TRUE)

Arguments

x

A list that provides model parameters and optionally meta data; use output of vst function

data

The name of the entry in x that holds the data

cell_attr

Provide cell meta data holding latent data info

do_round

Round the result to integers

do_pos

Set negative values in the result to zero

show_progress

Whether to print progress bar

Value

De-noised data as UMI counts

Examples

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vst_out <- vst(pbmc, return_cell_attr = TRUE)
umi_denoised <- denoise(vst_out)

sctransform documentation built on Nov. 18, 2018, 5:04 p.m.