transcript_shape_profile-class: Class transcript_shape_profile
In CshlSiepelLab/DENR: Deconvolution of Expression for Nascent RNA Sequencing Data

Description Slots

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.

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