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

View source: R/geomx_import_data.R

readGeoMxR Documentation

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.