Extract NCSLC dataset and make as data package

[maddygriz]

Duplicated Issue to GeomxTools iss141

SpatialDecon has a GeoMx NSCLC dataset that had an ROI placement strategy to mimic Visium data (55 um circles evenly placed).

This dataset is used in the GeomxTools coercion vignette. Creating a data package from this dataset would be nice. This is an older dataset so the names of columns need to be updated

Code to update column names:

data("nsclc", package = "SpatialDecon")
nsclc@featureType <- "Target"

colnames(protocolData(nsclc))[colnames(protocolData(nsclc)) == "NormFactorQ3"] <- "qFactors"
colnames(protocolData(nsclc))[colnames(protocolData(nsclc)) == "NormFactorHK"] <- "hkFactors"

colnames(protocolData(nsclc))[colnames(protocolData(nsclc)) == "RawReads"] <- "Raw"
colnames(protocolData(nsclc))[colnames(protocolData(nsclc)) == "TrimmedReads"] <- "Trimmed"
colnames(protocolData(nsclc))[colnames(protocolData(nsclc)) == "AlignedReads"] <- "Aligned"
colnames(protocolData(nsclc))[colnames(protocolData(nsclc)) == "StitchedReads"] <- "Stitched"
colnames(protocolData(nsclc))[colnames(protocolData(nsclc)) == "SequencingSaturation"] <- "Saturated (%)"

protocolData(nsclc) <- protocolData(nsclc)[,-which(colnames(protocolData(nsclc)) %in% c("UID"))]