miQC: fix "undefined columns selected" if column renamed

[kew24]

Users can choose their own percent.mt column name to fetch from their data, and the resulting column is subsequently renamed in as "percent.mt" in my_data:

seurat-wrappers/R/miqc.R

Lines 57 to 58 in 8d46d6c

	my_data <- Seurat::FetchData(object, vars = c(percent.mt, nFeature_RNA))
	colnames(my_data) <- c("percent.mt", "nFeature_RNA")

However, when subsetting on lines 120 & 126 (if the else if conditions of lines 117-127 are met), we get "undefined columns selected" errors if the user passed in anything other than the default to percent.mt – because we're subsetting using the value stored in the percent.mt variable:

seurat-wrappers/R/miqc.R

Lines 117 to 127 in 8d46d6c

	else if (backup.option == "percentile") {
	message("defaulting to backup.percentile for filtering")
	compromised_probability <- 0
	raw_values <- my_data[,percent.mt]
	percentile_cutoff <- quantile(raw_values, probs = backup.percentile)
	cells_to_keep <- ifelse(raw_values <= percentile_cutoff, "keep", "discard")}
	else if (backup.option == "percent"){
	message("defaulting to backup.percent for filtering")
	compromised_probability <- 0
	raw_values <- my_data[,percent.mt]
	cells_to_keep <- ifelse(raw_values <= backup.percent, "keep", "discard")}

Solutions include either reassigning percent.mt <- "percent.mt" after line 58, or subsetting on line 120 & 126 with the character value "percent.mt" that we've forced the column to be named as. I chose the latter of these two options.

Let me know if you have any comments, and feel free to edit if necessary. Thanks!