Get Outlier Genes

Identifies outlier genes from multiple cancer datasets. Treats the top 5 expressed genes in each sample as outliers and returns unique outlier genes.

Usage

GetOutlierGenes(cancers)

Arguments

cancers

Data frame. One column containing paths to gene expression files.

Value

Vector of unique gene names identified as outliers.

Examples

tf1 <- tempfile(fileext = ".tsv")
tf2 <- tempfile(fileext = ".tsv")

expr1 <- data.frame(
  gene = c("GeneA", "GeneB", "GeneC", "GeneD", "GeneE", "GeneF"),
  Sample1 = c(10, 50, 30, 80, 60, 20),
  Sample2 = c(15, 40, 25, 90, 55, 10)
)

expr2 <- data.frame(
  gene = c("GeneA", "GeneB", "GeneC", "GeneD", "GeneE", "GeneF"),
  Sample3 = c(100, 20, 10, 60, 30, 80),
  Sample4 = c(95, 25, 15, 70, 35, 85)
)

write.table(expr1, tf1, sep = "\t", row.names = FALSE, quote = FALSE)
write.table(expr2, tf2, sep = "\t", row.names = FALSE, quote = FALSE)

cancers <- data.frame(ExpressionFiles = c(tf1, tf2))
outlier_genes <- GetOutlierGenes(cancers)