transcript_quantifier-class: Class transcript_quantifier

In CshlSiepelLab/DENR: Deconvolution of Expression for Nascent RNA Sequencing Data

Description

Class transcript_quantifier holds encodings for each transcript and can be augmented to include data and transcript abundance estimates using the fit() function

Slots

transcripts

a GRanges-class that holds all the transcript coordinates

column_identifiers

a two element character vector that holds the column names in transcripts for the trancript and gene identifiers respectively. Only a column for the transcript identifier is required, missing gene identifiers are set to NA.

bins

a GRangesList-class object that records the bins for each group of transcripts

bin_size

width of bins used to create transcript models

models

a list of matrices with numeric values between 0 and 1 representing the fractional overlap of per transcript per bin where the rows are the transcripts and the columns are the bins. Rownames are the corresponding transcripts

masks

a list of matrices with numeric values between 0 and 1 that are used to modify the models

transcript_model_key

A three column data.frame that maps transcripts to their group and model

counts

a list of vectors containing the read counts per bin. Initialized empty.

upstream_polymerase_ratios

the log2 ratio of mean counts for each transcript from the region immediately upstream and downstream of each TSS; log2([500bp, 5.5kb] / [-5.5kb, -500bp])

tx_gof_metrics

some crude per transcript goodness-of-fit metrics that are used for heuristics in the fitting step

count_metadata

holds information about the files the count data came from including names and total counts

model_abundance

A list of vectors corresponding to models of transcript abundances. Initialized at 0.

CshlSiepelLab/DENR documentation built on July 16, 2021, 10:42 p.m.