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Load csv files from GenomeCov and their associated metadata. Create a RiboClass.

Source: R/load_ribodata.R
load_ribodata.Rd

Import your count CSV files and the metadata to create a RiboClass. The RiboClass is used by rRMSAnalyzer package for all analyses.

This function serves as the entrypoint of rRMSAnalyzer.

Usage

load_ribodata(
  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,
  flanking = 6,
  method = "median",
  ncores = 1
)

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.

flanking

Size of the local coverage.

method

Computation method of the local coverage. Either 'median' or 'mean'.

ncores

Number of cores to use in case of multithreading.

Value

a RiboClass

Details

load_ribodata is a wrapper of new_riboclass and compute_cscore.

See also

new_riboclass