rnaseq: Create an RNASeq experiment object
In openanalytics/ganalyse: Easy Analysis of RNASeq DE

Description Usage Arguments Details Value See Also Examples

Loads all sample info related to an experiment on to an object of class fpkm or raw.

1 2	rnaseq(sample_info, experiment = "example", format = c("fpkm", "raw"), verbose = FALSE)

`sample_info`	Complete path to file that contains `sample` names, columns that identify the `groups` each `sample` belongs to and path to the file that contains read counts for each sample. See `details` section for more.
`experiment`	Name of the experiment. Default is "example".
`format`	Is the input data `fpkm` or `raw` counts?
`verbose`	Logical. Default is `FALSE`. If `TRUE`, sends useful status messages to the console.

The file provided to sample_info (say annotation.txt) must have columns named sample (corresponding to sample names) and path (containing the file path to raw or fpkm counts). The path for each sample can either be a complete path or just the filename (with extension). If it is just a file name, it is assumed to be in the same path as annotation.txt.

The other columns usually identify which groups and/or treatments each sample belongs to. This allows easy construction of design matrix to describe treatment conditions later on, with the help of construct_design. These columns are optional at this point and can be added manually later on as well.

The easiest way would be to place annotation.txt and the counts in the folder.

An object of class fpkm or raw. It inherits from data.table.

gather_counts show_counts limma_dge edger_dge construct_design construct_contrasts write_dge as.dgelist as.eset volcano_plot density_plot

path = system.file("tests", package="ganalyse")

# ----- fpkm ----- # 
fpkm_path = file.path(path, "fpkm", "annotation.txt")
(fpkm_obj = rnaseq(fpkm_path, format="fpkm", experiment="sample"))
class(fpkm_obj)

# ----- raw ----- # 
raw_path = file.path(path, "raw", "annotation.txt")
(raw_obj = rnaseq(raw_path, format="raw", experiment="sample"))
class(raw_obj)