readGeoMx: Import GeoMX DSP data into a saptial experiment object from...

In DavisLaboratory/standR: Spatial transcriptome analyses of Nanostring's DSP data in R

Import GeoMX DSP data into a saptial experiment object from file paths

Description

Import GeoMX DSP data into a saptial experiment object from file paths

Usage

readGeoMx(
  countFile,
  sampleAnnoFile,
  featureAnnoFile = NA,
  rmNegProbe = TRUE,
  NegProbeName = "NegProbe-WTX",
  colnames.as.rownames = c("TargetName", "SegmentDisplayName", "TargetName"),
  coord.colnames = c("ROICoordinateX", "ROICoordinateY")
)

Arguments

countFile	tsv file or a dataframe object. Count matrix, with samples in columns and features/genes in rows. The first column is gene names/ids.
sampleAnnoFile	tsv file or a dataframe object. Sample annotations.
featureAnnoFile	tsv file or a dataframe object. Feature/Gene annotations.
rmNegProbe	Logical. Default is TRUE, indicating there are negative probe genes in the data.
NegProbeName	Character. Name of negative probe genes, default is NegProbe-WTX.
colnames.as.rownames	Vector of characters, length of 3. Column names used to capture gene names, sample names and gene names in countFile, sampleAnnoFile and featureAnnoFile, respectively.
coord.colnames	Vector of characters, length of 2. Column names used to capture ROI coordinates.

Value

A SpatialExperiment object.

Examples

library(ExperimentHub)

eh <- ExperimentHub()
query(eh, "standR")
countFile <- eh[["EH7364"]]
sampleAnnoFile <- eh[["EH7365"]]

spe <- readGeoMx(countFile, sampleAnnoFile, rmNegProbe = FALSE)

DavisLaboratory/standR documentation built on Sept. 8, 2024, 9:57 p.m.