annotate.electrophoresis: Add annotations to an electrophoresis object

In jwfoley/bioanalyzeR: Analysis of Agilent electrophoresis data

Add annotations to an electrophoresis object

Description

This function adds columns of annotations to the $samples table of an electrophoresis object. These new annotations can be used for subsetting, plot faceting, etc.

Usage

annotate.electrophoresis(
  electrophoresis,
  annotations,
  header = TRUE,
  row.names = NULL,
  sep = "\t",
  stringsAsFactors = TRUE,
  ...
)

Arguments

electrophoresis	An electrophoresis object.
...	Additional arguments passed to read.table.
annotation	Either a data frame or the path of a file that can be read by read.table.

Details

The input annotations can be a data frame or either a connection or a character containing the path of a file, which is then read into a data frame by read.table. Therefore a file will probably need to be in CSV format or similar.

The first column of annotations is used to identify samples in the matching column of electrophoresis$samples, so it needs a matching column name, usually sample.name or well.number. But you can use any column that exists in the table, such as batch or reagent.id or even a column added by a previous call to this function. The elements of this first column are interpreted as class character and cannot contain any duplicates. However, this column does not need to be in the same order as electrophoresis$samples and not all identifiers in the sample table (e.g. sample names) need to appear in the annotation table, nor vice versa.

Each additional column of annotations produces a new column of the same name in electrophoresis$samples. If there is already a column of that name, it is overwritten. Samples that do not appear in the annotation table receive NA for their new annotations. Samples with the same identifier (e.g. the same sample.name because they are replicates) receive the same annotations.

If stringsAsFactors is true then variables parsed as strings will be cast as factors, but the factor levels will be kept in the order they appear in the table, unlike the behavior of read.table, which alphabetizes them. Thus the order in the annotation file determines the order of factor levels.

Value

A new electrophoresis object with additional columns added to its $samples element.

jwfoley/bioanalyzeR documentation built on Aug. 1, 2023, 4:46 a.m.