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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
)

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.