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Get normalized read counts from either a cB table or EZbakRFractions object.

get_normalized_read_counts.Rd

Uses TMM normalization strategy, similar to that used by DESeq2 and edgeR.

Usage

get_normalized_read_counts(
  obj,
  features_to_analyze,
  fractions_name = NULL,
  feature_lengths = NULL
)

# S3 method for class 'EZbakRFractions'
get_normalized_read_counts(
  obj,
  features_to_analyze,
  fractions_name = NULL,
  feature_lengths = NULL
)

# S3 method for class 'EZbakRData'
get_normalized_read_counts(
  obj,
  features_to_analyze,
  fractions_name = NULL,
  feature_lengths = NULL
)

Arguments

obj

An EZbakRData or EZbakRFractions object.

features_to_analyze

Features in relevant table

fractions_name

Name of fractions table to use

feature_lengths

Table of effective lengths for each feature combination in your data. For example, if your analysis includes features named GF and XF, this should be a data frame with columns GF, XF, and length.

Value

Data table of normalized read counts.

Methods (by class)

  • get_normalized_read_counts(EZbakRFractions): Method for class EZbakRFractions Get normalized read counts from fractions table.

  • get_normalized_read_counts(EZbakRData): Method for class EZbakRData Get normalized read counts from a cB table.

Examples


# Simulate data
simdata <- EZSimulate(30)

# Create EZbakRData object
ezbdo <- EZbakRData(simdata$cB, simdata$metadf)

# Get normalized read counts
reads <- get_normalized_read_counts(ezbdo, features_to_analyze = "feature")