romicsCreateObject: romicsCreateObject()

In PNNL-Comp-Mass-Spec/RomicsProcessor: omics-oriented package for reproducible and sharable data processing pipelines

romicsCreateObject()

Description

Create a romics_object by combining a data and a metadata data frames

Usage

romicsCreateObject(
  data,
  metadata,
  IDs,
  main_factor = "none",
  custom_colors = ROP_colors,
  omics_type = "unknown",
  quantif_type = "unknown"
)

Arguments

data	A data frame corresponding to the data.
metadata	A data frame corresponding to the metadata, the columns must be the same as the data ones.
IDs	A data frame corresponding to the list of alternative IDs for the romics_object, this enables to use human readable ids for certain plots. The first column contains the same type of IDs as the imported data.
main_factor	The rowname of a metadata factor, by default the first row will be used as main factor.
custom_colors	A character vector containing the colors you want to use for your figures generated from an romics_object.
omics_type	A character vector of length 1 indicating the type of omics data used.
quantif_type	A character vector of length 1 indicating the type of quantification performed.

Value

This function generate an romics_object containing the following layers : data, metadata, missingdata, original_data, main_factor, colors, steps, custom_colors, omics_type, quantif_type

Author(s)

Geremy Clair

Examples

ROP_romics_object <- romicsCreateObject(ROP_data,ROP_metadata,main_factor="condition")

PNNL-Comp-Mass-Spec/RomicsProcessor documentation built on March 18, 2023, 5:14 a.m.