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

View source: R/transcript_quantifier-class.R

Contructs an object that holds the transcript models

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")
)

`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").