Read ribomethseq count files and their associated metadata and merge them into a RiboClass. This is the constructor of the RiboClass S3 class. All other functions use the RiboClass as an input.
The constructor cannot be called directly. To create a RiboClass, please use load_ribodata.
Usage
new_riboclass(
count_path,
metadata = NULL,
count_sep = "\t",
metadata_sep = ",",
count_header = FALSE,
count_value = 3,
count_rnaid = 1,
count_pos = 2,
metadata_key = "filename",
metadata_id = NULL
)Arguments
- count_path
(required) path to the data folder containing count files.
- metadata
Data frame or path to a CSV file containing metadata.
- count_sep
Delimiter used for the CSV files.
- metadata_sep
Delimiter used in metadata (if imported from file).
- count_header
Boolean, specify if count files have a header or not.
- count_value
Name or index of the column containing count values.
- count_rnaid
Name or index of the column containing the name of the RNA in count data.
- count_pos
Name or index of the column containing the site's position in count data.
- metadata_key
(required when metadata not null) Name or index of the column containing the samples' filename.
- metadata_id
Name or index of the column containing the sample name.
Details
The RiboClass object is a S3 Class with three elements :
data : a list of dataframe, each corresponding to a sample. Each dataframe starts with the following columns :
rna : the name of the RNA for a given position.
rnapos : the position on the current RNA.
count : the number of read starting (5'end) or ending (3'end) at this position.
site : the name of the site, which will be empty after the RiboClass creation. To fill this column, use
annotate_site.
metadata : a dataframe containing all information related to each sample.
This is particularly useful for technical biases correction (with adjust_bias) and plot functions (for coloring or add an extra layer of informations).
If no metadata are given, an empty one will be generated.
rna_names : a dataframe containing original and current rna names.
The name of RNAs can be renamed for the sake of clarity on plots (with rename_rna), but the original ones can contain important information, like NCBI ID.
the path given in count_path should contains only necessary CSV files (one per sample). While the directory structure is not important, make sure each sample has an unique filename.
The path to the csv file or the dataframe given in metadata must contains a filename column, as this will serve to link metadata with the dataframes in data during the RiboClass creation.