CreatespaceSTobject: Initiialize and setup the spaceST object

Description Usage Arguments Value

View source: R/preprocessing.R

Description

Initialized the spaceST object from an expression matrix with genes as rows and array coordinates as columns. When the object is initialized, some optional filtering settings can be applied to remove genes and/or spots of low quality.

Usage

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CreatespaceSTobject(raw.data, unique.genes = 0, min.exp = 0,
  min.features = 0, filter.genes = NULL, delimiter = "_")

Arguments

raw.data

A list of expression matrices/data.frames with genes as rows and feature coordinates as columns. Headers should be formatted with a unique symbol, x, and y coordinate seperated by a delimiter.

unique.genes

The lowest number of unique genes allowed in a feature.

min.exp

Integer value specifying the lowest expression value allowed at least min.features number of features.

min.features

Integer value specifying the lowest number of features with at least min.exp.

filter.genes

A character vector specifying genes that should be filtered from the expression data.

delimiter

Delimiter specifying header format.

Value

A spaceST object containing a merged expression matrix of gene expression counts.


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