spaceST-methods: space-ST methods.

In ludvigla/spaceST: spaceST

Description

Normalization of gene expression data using either counts per 10k or scran.

Plot principal components.

Plot t-SNE.

Usage

## S4 method for signature 'spaceST'
batch.correct(object)

NormalizespaceST(object, method = "scran", log2 = F, pcount = 1,
  clusters = NULL)

## S4 method for signature 'spaceST'
NormalizespaceST(object, method = "cp10k",
  log2 = F, pcount = 1, clusters = NULL)

plotPCA(object, components = c(1, 2), ...)

## S4 method for signature 'spaceST'
plotPCA(object, components = c(1, 2), ...)

plotTSNE(object, group_by = NULL, cols = NULL, ...)

## S4 method for signature 'spaceST'
plotTSNE(object, group_by = NULL, cols = NULL, ...)

## S4 method for signature 'spaceST'
plot_QC_spaceST(object, separate = F, bins = 20,
  type = "norm.data", ...)

## S4 method for signature 'spaceST'
spPCA(object, ntop = 500,
  exprs_values = "norm.data", ...)

## S4 method for signature 'spaceST'
spots_under_tissue(object, selection.files,
  delimiter = "_", keep.filter = T)

## S4 method for signature 'spaceST'
filter(object, unique.genes = 300, min.exp = 2,
  min.features = 15, filter.genes = NULL, force.filter = FALSE,
  delimiter = "_")

## S4 method for signature 'spaceST'
dim(x)

## S4 method for signature 'spaceST'
counts(object)

## S4 method for signature 'spaceST'
normcounts(object)

## S4 method for signature 'spaceST'
topic.clusters(object)

## S4 method for signature 'spaceST'
getLDA(object)

Arguments

object	Object of class spaceST.
method	Select normalization method, default "cp10k" [options: "cp10k", "scran"].
log2	Logical specifying whether or not data should be log2-transformed.
pcount	Pseudocount value for log2 tranformation (default = 1).
clusters	Integer vector specifying clusters used for normalization with scran on large gene expression matrices. By default, a clustering step is performed using quickCluster if there are more than 500 array spots in the expression matrix.
components	Integer or character vector of length 2 specifying two PC components to compare.
...	Parameters passed to geom_point().
group_by	character; Grouping variable for color.
cols	character; Specify colors for grouping variable.
object	Object of class spaceST.
object	Object of class spaceST.
object	Object of class spaceST.
...	Parameters passed to geom_point().
object	Object of class spaceST.
object	Object of class spaceST.
object	Object of class spaceST.
object	Object of class spaceST.

Value

Normalized expression data.

PCA plot.

t-SNE plot.

See Also

normalize and computeSumFactors

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