disj_background: Find the background of the user provided mod_gration.
In exomePeak2: Bias Awared Peak Calling and Quantification for MeRIP-Seq

Find the background of the user provided mod_gration.

disj_background(
  mod_gr,
  txdb,
  background_bins = NULL,
  background_types = c("Gaussian_mixture", "m6Aseq_prior", "manual", "all"),
  control_width = 50,
  rename_mod = FALSE
)

`mod_gr`	A `GRanges` object of user provided mod_gration (names are neccessary for the index of the splitting).
`txdb`	A `TxDb` object that define the transcript mod_gration.
`background_bins`	A Granges object for background binds.
`background_types`	A logical value, TRUE if the region of 5'UTR and long exons of the transcripts should be dropped in control region; Default TRUE.
`control_width`	A integer for the minimum width of the control region returned; default 50.
`rename_mod`	Whether to rename the returned modification sites, default = FALSE.

A GRangesList object. The first portion is the exons regions that is not overlapped with annoation.

If the resulting ranges have less number and width compared with what defined in cut_off_num, the exon regions of txdb will be returned as the background.

The second portion is the restructed user provided mod_gration with gene id mod_grated.

exomePeak2 documentation built on Nov. 8, 2020, 5:27 p.m.