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Gene expression in human embryonic stem cells

Source: R/hESC_expression.R
hESC_expression.Rd

Plots a heatmap of genes expression in human embryonic stem cells, using RNAseq data downloaded from Encode database.

Usage

hESC_expression(
  genes = NULL,
  include_CTP = FALSE,
  units = c("TPM"),
  scale_lims = NULL,
  values_only = FALSE
)

Arguments

genes

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

include_CTP

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

units

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

scale_lims

vector of length 2 setting the lower and upper limits of the heatmap colorbar. By default, the lower limit is 0, and the upper limit corresponds to the third quartile of the logcounts values.

values_only

logical(1). If TRUE, the function will return the SingleCellExperiment instead of the heatmap. Default is FALSE.

Value

A heatmap of selected CT genes expression in single cells from human embryonic stem cells. If values_only = TRUE, a SummarizedExperiment is returned instead.

Examples

if (FALSE) { # \dontrun{
hESC_expression(include_CTP = FALSE, units = "log_TPM",
                  values_only = FALSE)
} # }