metaData: Declare meta data information for downstream analysis

In jcardenas14/genBART: Generate 'BART' File

Description

Match design and expression data frames. Declare and store design parameters.

Usage

metaData(y, design, data.type = "rnaseq", columnname = NULL, long = FALSE,
  time.var = NULL, sample.id = NULL, subject.id = NULL,
  baseline.var = NULL, baseline.val = NULL, control.var = NULL,
  control.val = NULL)

Arguments

y	An expression data frame.
design	A sample annotation data frame containing sample information (e.g. age, condition, timepoint, etc.).
data.type	Type of data that's going to be analyzed ("rnaseq", "microarray","flow", "metab"). Default is data.type="rnaseq".
columnname	Name of column in design that contains the column names of y.
long	logical; Is the study longitudinal?.
time.var	For longitudinal studies. Name of column in design that contains the study time points.
sample.id	Name of column in design that contains unique sample identification.
subject.id	Name of column in design that contains ids for individual subjects.
baseline.var	Name of column in design that contains values referring to baseline observations.
baseline.val	String or numeric value denoting baseline observations.
control.var	Name of column in design that contains values referring to controls.
control.val	String or numeric value denoting controls.

Value

A list containing the matched design and expression data and all of the design parameters specified.

Examples

# Using example data
data(tb.expr)
data(tb.design)
meta.data <- metaData(y = tb.expr, design = tb.design, data.type = "microarray", 
                    columnname = "columnname", long = TRUE, sample.id = "sample_id",
                    subject.id = "monkey_id", time.var = "timepoint",
                    baseline.var = "timepoint", baseline.val = 0)

jcardenas14/genBART documentation built on May 8, 2019, 5:49 p.m.