transcript_shape_profile: Creates transcript_shape_profile

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

Description

Creates object of transcript_shape_profile, which holds data for a set of transcripts that are used to generate an empirical shape profile. That shape profile can then be used with modify_model to alter the models in a transcript_quantifier object. To get the list of transcripts to create the shape profile a series of filters are applied and then the longest of the remaining transcripts for each overlapping set of transcripts is chosen. Then each transcript is binned and ...

Usage

transcript_shape_profile(
  transcripts,
  bigwig_plus = NULL,
  bigwig_minus = NULL,
  bin_size = 250,
  min_percent_transcribed = 0.8,
  min_transcript_length = 8000,
  percent_model_match = 0.8,
  linear_head_length = 10000,
  linear_tail_length = 5000,
  span = 0.4
)

Arguments

transcripts	a GRanges-class object that contains the ranges of potential transcripts to be used to fit an empirical shape profile. This list will be filtered using the criteria specified by the min_transcript_length, max_group_size, and percent_model_match parameters
bigwig_plus	the path to a bigwig for reads on the plus strand
bigwig_minus	the path to a bigwig for reads on the minus strand
bin_size	width of each position range that is being converted
min_percent_transcribed	all transcripts with pro-seq signal for less than this percent of the transcript are removed
min_transcript_length	all transcripts shorter than this are removed from consideration (default: 5e3)
percent_model_match	Based on the transcript ranges for each transcript certain regions are expected to contain nascent RNAP signal or not. For each transcript the percent agreement with that expectation is computed and all transcripts below that are removed (default: 0.8).
linear_head_length	total width of head region (# of bins * width)
linear_tail_length	total width of tail region (# of bins * width)
span	the parameter α which controls the degree of smoothing.

CshlSiepelLab/tuSelecter2 documentation built on July 18, 2021, 5:09 p.m.