com_factor {spatialHeatmap} | R Documentation

## Combine Factors in Targets File

### Description

This is a helper function for data/aSVGs involving three or more factors such as sample, time, condition. It combine factors in targets file to make composite factors.

### Usage

    com_factor(se, target, factors2com, sep = ".", factor.new)

### Arguments

`se` | A `SummarizedExperiment` object.
`target` | A `data.frame` object of targets file.
`factors2com` | A character vector of column names or a numeric vector of column indeces in the targets file. Entries in these columns are combined.
`sep` | The separator in the combined factors. One of `_`, and `.` (default).
`factor.new` | The column name of the new combined factors.

### Value

If `se` is provided, a `SummarizedExperiment` object is returned, where the `colData` slot contains the new column of combined factors. Otherwise, a`data.frame` object is returned, where the new column of combined factors is appended.

### Author(s)

Jianhai Zhang jzhan067@ucr.edu; zhang.jianhai@hotmail.com
Dr. Thomas Girke thomas.girke@ucr.edu

### References

Narsai, Reena, David Secco, Matthew D Schultz, Joseph R Ecker, Ryan Lister, and James Whelan. 2017. "Dynamic and Rapid Changes in the Transcriptome and Epigenome During Germination and in Developing Rice (Oryza Sativa) Coleoptiles Under Anoxia and Re-Oxygenation." Plant J. 89 (4): 805–24

### Examples

    clp.tar <- system.file('extdata/shinyApp/example/target_coleoptile.txt', package='spatialHeatmap')
    target.clp <- read_fr(clp.tar)
    target.clp <- com_factor(target=target.clp, factors2com=c('organism_part', 'age'), factor.new='samTime')

[Package spatialHeatmap version 1.2.0 Index]