GetData {grandR}

Obtain a tidy table of values for a gene or a small set of genes

Description

This is the main function to access slot data data from a particular gene (or a small set of genes) as a tidy table. If data for all genes must be retrieved (as a large matrix), use the GetTable function. For analysis results, use the GetAnalysisTable function.

Usage

GetData(
  data,
  mode.slot = DefaultSlot(data),
  columns = NULL,
  genes = Genes(data),
  by.rows = FALSE,
  coldata = TRUE,
  ntr.na = TRUE,
  name.by = "Symbol"
)

Arguments

data

A grandR object

mode.slot

Which kind of data to access (see details)

columns

A vector of columns (see details); all condition/cell names if NULL

genes

Restrict the output table to the given genes (this typically is a single gene, or very few genes)

by.rows

if TRUE, add rows if there are multiple genes / mode.slots; otherwise, additional columns are appended

coldata

Should the table contain the Coldata values as well (at the beginning)?

ntr.na

For columns representing a 4sU naive sample, should mode.slot ntr,new.count and old.count be 0,0 and count (ntr.na=FALSE; can be any other slot than count) or NA,NA and NA (ntr.na=TRUE)

name.by

A column name of Coldata(data). This is used as the colnames of the output table

Details

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 obtain the new counts.

If only one mode.slot and one gene is given, the output table contains one column (and potentially columns from Coldata) named Value. If one gene and multiple mode.slots are given, the columns are named according to the mode.slots. If one mode.slot and multiple genes are given, the columns are named according to the genes. If multiple genes and mode.slots are given, columns are named gene.mode.slot.

If by.rows=TRUE, the table is molten such that each row contains only one value (for one of the genes and for one of the mode.slots). If only one gene and one mode.slot is given, melting does not have an effect.

Columns can be given as a logical, integer or character vector representing a selection of the columns (samples or cells). The expression is evaluated in an environment havin the Coldata, i.e. you can use names of Coldata as variables to conveniently build a logical vector (e.g., columns=Condition=="x").

Value

A data frame containing the desired values

See Also

GetTable,GetAnalysisTable,DefaultSlot,Genes

Examples

sars <- ReadGRAND(system.file("extdata", "sars.tsv.gz", package = "grandR"),
                  design=c("Cell",Design$dur.4sU,Design$Replicate))
GetData(sars,mode.slot="ntr",gene="MYC")
# one gene, one mode.slot
GetData(sars,mode.slot=c("count","ntr"),gene="MYC",coldata = FALSE)
# one gene, multiple mode.slots
GetData(sars,mode.slot=c("count","ntr"),gene=c("SRSF6","MYC"),by.rows=TRUE)
# multiple genes, multiple mode.slots, by rows