addtrack: Add gene coordinate track to a gene's rate inference result...

In yuabrahamliu/proRate: proRate is an R package to infer gene transcription rates with a novel least sum of squares method.

Add gene coordinate track to a gene's rate inference result plot

Description

Add gene coordinate track to a gene's rate inference result plot generated by the function calrate or mcalrate.

Usage

addtrack(
  genedat,
  binplotdat,
  expandplotdat,
  genomename = "mm10",
  textsize = 13,
  titlesize = 15,
  face = "bold",
  method = NULL
)

Arguments

genedat	The gene rate inference report data frame generated by the function calrate or mcalrate. It can be extracted from the "report" slot of these functions' result, which is a data frame, and what needed here is the its sub-data-frame (with only one row) containing the result information of the specific gene whose inference plots need to be modified here.
binplotdat	The bin-level rate inference plot data of a specific gene. It can be extracted from the "binplots" slot of the results generated by calrate or mcalrate. What needed here is the element data contained in this slot using the gene's name as the element name.
expandplotdat	The base-pair-level rate inference plot data of a gene. It can be extracted from the "expandplots" slot of the results generated by the function calrate or mcalrate. What needed here is the element data contained in this slot using the gene's name as the element name.
genomename	Specify the genome of the specific gene whose inference plots need to be modified here. It can be "mm10" for mouse or "hg38" for human.
textsize	The font size for the plot texts. Default is 13.
titlesize	The font size for the plot titles. Default is 15.
face	The font face for the plot texts. Default is "bold".
method	The method used when inferring the gene's transcription rate with the function calrate or mcalrate. Can be "LSS" for the least sum of squares method, or "HMM" for the hidden Markov model method.

Value

The modified gene rate inference plots with the gene's coordinate track added.

Examples

library(proRate)

wt0file <- system.file("extdata", "wt0.bam", package = "proRate")
wt15file <- system.file("extdata", "wt15.bam", package = "proRate")

wtrates <- calrate(time1file = wt0file, 
                  time2file = wt15file, 
                  time = 15, 
                  strandmethod = 1, 
                  
                  genomename = "mm10", 
                  lencutoff = 40000, 
                  fpkmcutoff = 1, 
                  
                  threads = 4, 
                  
                  startshorten = 1000, 
                  endshorten = 1000, 
                  window_num = 40, 
                  
                  method = "LSS", 
                  pythonpath = NULL, 
                  
                  difftype = 1)

addtrack(genedat = subset(wtrates$report, gene_id == "Mamdc2"), 
        binplotdat = wtrates$binplots$Mamdc2, 
        expandplotdat = wtrates$expandplots$Mamdc2, 
        genomename = "mm10", 
        method = "LSS", 
        titlesize = 17, 
        textsize = 16, 
        face = "bold")

yuabrahamliu/proRate documentation built on Nov. 3, 2024, 10:14 a.m.