metaData: Declare meta data information for downstream analysis

Description Usage Arguments Value Examples

View source: R/metaData.R

Description

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

Usage

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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

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# 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)

genBart documentation built on March 18, 2018, 2:11 p.m.