serp_data_accessors: Accessors for 'serp_data' objects

In ilia-kats/RiboSeqTools: Tools for analysis of selective ribosome profiling (SeRP) data

Description

Accessors for serp_data objects

Usage

## S3 method for class 'serp_data'
get_data(data)

experiments(data)

samples(data)

## S3 method for class 'serp_data'
get_reference(data)

## S3 method for class 'serp_data'
get_total_counts(data, as_df = FALSE)

## S3 method for class 'serp_data'
get_defaults(data)

## S3 method for class 'serp_data'
is_normalized(data)

is_downsampled(data)

## S3 method for class 'serp_data'
excluded(data)

get_background_model(data)

get_binding_pvalues(data)

Arguments

data	A serp_data object.

Value

get_data

Nested named list, with first level representing the experiment, second level the replicate, third level the sample type, and fourth level the binning. Count tables are sparse matrices with each row corresponding to an ORF.

experiments

Character vector containing names of experiments in the data set.

samples

Character vector containing names of all samples present in the data set.

get_reference

Reference data frame. Guaranteed to contain at least the following columns:

gene

Gene/ORF name. Must match the names given in the read count tables.

length

ORF length in nucleotides.

cds_length

ORF length in codons.

get_total_counts

Nested named list containing toal read counts for each sample. If as_df is TRUE, returns a tibble instead.

get_defaults

Named list of default parameters for this data set.

get_background_model

Background model estimated by fit_background_model.

get_binding_pvalues

Binding p-values calculated by test_binding.

is_normalized

A logical value indicating whether the data object contains raw or normalized read counts.

is_downsampled	A logical value indicating whether the data object has been downsampled to the lowest total read counts by downsample.
excluded	Character vector of genes excluded from analyses.

ilia-kats/RiboSeqTools documentation built on Oct. 5, 2020, 7:41 p.m.