computeProjectionGenes: filter data accourding to the provided filters

Description Usage Arguments Value

View source: R/AnalysisFunctions.R

Description

filter data accourding to the provided filters

Usage

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computeProjectionGenes(
  object,
  threshold = NULL,
  num_mad = NULL,
  projection_genes_method = NULL,
  projection_genes = NULL
)

Arguments

object

the VISION object

threshold

Threshold to apply when using the 'threshold' or 'fano' projection genes filter. If greater than 1, this specifies the number of cells in which a gene must be detected for it to be used when computing PCA. If less than 1, this instead specifies the proportion of cells needed

num_mad

Number of median absolute deviations to use when selecting highly-variable genes in each mean-sorted bin of genes

projection_genes_method

a method to select genes either 'Threshold' or 'Fano'

projection_genes

a list of genes to use specifically. If this is supplied then 'projection_genes_method' is ignored

Value

the VISION object, populated with filtered data


YosefLab/VISION documentation built on Sept. 14, 2021, 5:27 p.m.