ComputeExpressionPercentage {grandR}

Expression percentage computation

Description

Compute the expression percentage for a particular set of genes.

Usage

ComputeExpressionPercentage(
  data,
  name,
  genes = Genes(data),
  mode.slot = DefaultSlot(data),
  genes.total = Genes(data),
  mode.slot.total = mode.slot,
  multiply.by.100 = TRUE
)

Arguments

data

the grandR object

name

the new name by which this is added to the Coldata

genes

define the set of genes to compute the percentage for

mode.slot

which mode.slot to take the values for computing the percentage from

genes.total

define the set of genes defining the total value

mode.slot.total

which mode.slot to take the values for computing the total

multiply.by.100

if TRUE, compute percentage values, otherwise fractions between 0 and 1

Details

The percentages are computed for the given genes with the given mode.slot, w.r.t the mode.slot.total from the genes.total. Thus to compute the percentage of mitochondrial gene expression in total RNA (unnormalized), only set genes=Genes(data,"^MT-",regex=TRUE). To compute the percentage of new RNA among all genes, set mode.slot="new.count" and mode.slot.total="count".

Genes can be referred to by their names, symbols, row numbers in the gene table, or a logical vector referring to the gene table rows.

To refer to data slots, the mode.slot syntax can be used: Each name is either a data slot, or one of (new,old,total) followed by a dot followed by a slot. For new or old, the data slot value is multiplied by ntr or 1-ntr. This can be used e.g. to filter by new counts.

Value

a new grandR object having the expression percentage in its Coldata table

See Also

Coldata