LDA: Helper function to compute lda using cellTree package.

In ludvigla/spaceST: spaceST

Description

This helper function is used to compute topics for an expression dataset using lda modelling from cellTree package.

Usage

topic_compute(object, min.topic = 2, max.topic = 15,
  num.genes = NULL, datatype = "norm.data", method = "maptpx",
  sd.filter = F, log.scale = F, force.recalc = F,
  minClusterSize = 30)

## Default S3 method:
topic_compute(object, min.topic = 2, max.topic = 15,
  num.genes = NULL, datatype = "norm.data", method = "maptpx",
  sd.filter = F, log.scale = F, force.recalc = F,
  minClusterSize = 30)

## S3 method for class 'spaceST'
topic_compute(object, min.topic = 2, max.topic = 15,
  num.genes = NULL, datatype = "norm.data", method = "maptpx",
  sd.filter = FALSE, log.scale = FALSE, force.recalc = FALSE,
  minClusterSize = 30)

Arguments

object	Object of class spaceST.
min.topic, max.topic	Integer values specifying min and max number of topics in the "maptpx" model.
num.genes	Number of genes to use for lda modelling.
datatype	Character string specifying if the "expr" or "norm.data" ata should be used as input. Default is set to "norm.data".
method	Method passed to CellTree function.
sd.filter	Standard deviation threshold.
log.scale	Convert to log scale.

Value

Topic matrix

References

https://bioconductor.org/packages/release/bioc/html/cellTree.html

See Also

compute.lda

ludvigla/spaceST documentation built on May 29, 2019, 3:43 a.m.