transcript_shape_profile-class: Class transcript_shape_profile

In CshlSiepelLab/tuSelecter2: Deconvolution of Expression for Nascent RNA Sequencing Data

Class transcript_shape_profile

Description

Class transcript_shape_profile holds data for a set of transcripts that are used to generate an empirical shape profile. Can be created by calling transcript_shape_profile. A shape profile can be used with modify_model to alter the models in a transcript_quantifier object.

Slots

transcripts

a GRanges-class object that contains the ranges of transcripts used to fit the empirical shape profile.

bin_size

bin size used to create transcript profile functions

linear_head_length

distance into gene from TSS that is treated as the head region for the purposes of position scaling

linear_tail_length

distance into gene from the transcript end that is treated as the tail region for the purposes of position scaling

head_percent

The head region of the gene is rescaled so the position vector that is paired with the count vector is between [0, head_percent]

tail_percent

The tail region of the gene is rescaled so the position vector that is paired with the count vector is between [1 - tail_percent, 1]

shape_profile

a loess function that is used to predict the shape profile

shape_scale_factor

a scalar value to multiply the output of the loess function by so that the profile factors predicted by the loess fit have a median value of 1 in the central body of the gene

CshlSiepelLab/tuSelecter2 documentation built on June 2, 2025, 7:09 a.m.