R: Get tidy-style data from 'TapestriExperiment' objects

getTidyData {karyotapR}

R Documentation

Get tidy-style data from `TapestriExperiment` objects

Description

getTidyData() pulls data from the indicated assay and/or altExp slot(s), and rearranges it into tidy format. colData (cell metadata) from the top-level/main experiment is included. rowData (probe metadata) from the indicated assay and/or altExp slot(s) is included. Attempts are made to sort by "chr" and "start.pos" columns if they are present to simplify plotting and other downstream operations.

Usage

getTidyData(
  TapestriExperiment,
  alt.exp = NULL,
  assay = NULL,
  feature.id.as.factor = TRUE
)

Arguments

`TapestriExperiment`	`TapestriExperiment` object.
`alt.exp`	Character, `altExp` slot to use. `NULL` (default) uses top-level/main experiment.
`assay`	Character, `assay` slot to use. `NULL` (default) uses first-indexed assay (often "counts").
`feature.id.as.factor`	Logical, if `TRUE` (default), the feature.id column is returned as a factor.

Value

A tibble of tidy data with corresponding metadata from colData and rowData.

Examples

tap.object <- newTapestriExperimentExample() # example TapestriExperiment object
tidy.data <- getTidyData(tap.object, alt.exp = "alleleFrequency")