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Gene expression in CCLE Tumors

Source: R/CCLE_expression.R
CCLE_expression.Rd

Plots an expression heatmap of genes in CCLE tumor cell lines.

Usage

CCLE_expression(
  genes = NULL,
  type = NULL,
  units = c("TPM", "log_TPM"),
  include_CTP = FALSE,
  values_only = FALSE
)

Arguments

genes

character naming the selected genes. The default value, NULL, takes all CT (specific) genes.

type

character() describing the tumor cell line(s) type to be plotted. Allowed cell lines are "Ovarian", "Leukemia", "Colorectal", "Skin", "Lung", "Bladder", "Kidney", "Breast", "Pancreatic", "Myeloma", "Brain", "Sarcoma", "Lymphoma", "Bone", "Neuroblastoma", "Gastric", "Uterine", "Head_and_Neck", "Bile_Duct" and "Esophageal".

units

character(1) with expression values unit. Can be "TPM" (default) or "log_TPM" (log(TPM + 1))

include_CTP

logical(1) If TRUE, CTP genes are included. (FALSE by default).

values_only

logical(1). If TRUE, values are returned instead of the heatmap (FALSE by default).

Value

A heatmap of selected genes in CCLE cell lines from specified type. If values_only is TRUE, expression values are returned instead.

Examples

if (FALSE) { # \dontrun{
CCLE_expression(
    genes = c("MAGEA1", "MAGEA3", "MAGEA4", "MAGEA6", "MAGEA10"),
    type = c("Skin", "Lung"), units = "log_TPM")
} # }