transcript_quantifier: transcript_quantifier

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

Description

Contructs an object that holds the transcript models

Usage

transcript_quantifier(
  transcripts,
  transcript_name_column,
  gene_name_column = NULL,
  bin_size = 250,
  distance = NULL,
  mask_start_bins = NULL,
  mask_end_bins = NULL,
  bin_operation = c("round", "floor", "ceiling")
)

Arguments

transcripts	a GRanges-class object that must contain a metadata column with a transcript id and may contain an additional column with a gene id
transcript_name_column	A string that indicates which column in the GRanges object contain the transcript names
gene_name_column	a string that indicates which column in the GRanges object contains the gene names (not required)
bin_size	An integer, used to tile the gene region. Default is 250bp.
distance	the distance within which two transcripts are considered connected (must be at least bin size, defaults to bin size). The smaller this value is the more efficiently the model can be fit. Only increase this if you are masking large regions at the starts and ends of genes.
mask_start_bins	A numeric vertor with length two which giving the number of bins should be masked near the start of a transcript. The first integer is the number of bins will be masked inside the transcript, while the second interger is the number outside the transcript. Default c(0, 0).
mask_end_bins	A numeric vertor with length two which giving the number of bins should be masked near the end of a transcript. The first integer is the number of bins will be masked inside the transcript, while the second interger is the number outside the transcript. Default c(0, 0).
bin_operation	Three different modes to deal with decimals in the transript model (due to partial overlap of the first or last exon and bins). Either "ceiling", "floor", or "round" (default: "round").

Value

an transcript_quantifier-class object

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