powerASEeQTL: powerASEeQTL
In SharonLutz/powerASEeQTL: This package runs a power analysis on RNAseq data

Description Usage Arguments Value Author(s)

View source: R/powerASEeQTL.R

This function implements a power analysis for RNAseq data and then plots it.

powerASEeQTL(n, mu = 500, n.simu = 200, sim = "sim1",
  methods = c("eQTL.linear", "eQTL.negBin", "eQTL.quasipoisson", "ASE",
  "eQTL.ASE"), folds = seq(1, 2, length.out = 3), alpha = 0.001,
  phi = 1.1, theta = 0.1, maf = 0.2, propASE = 0.005,
  legend = TRUE, color = TRUE, title = "", subtitle = "",
  titlecolor = "black", subtitlecolor = "black", titlesize = 1,
  subtitlesize = 1, labelsize = 1, labelcolor = "black",
  linewidth = 2, tilt = 0, SEED = 1)

`n`	denotes the sample size.
`mu`	denotes the total number of reads.
`n.simu`	denotes the number of simulations.
`sim`	denotes the type of way the data is simulated.
`methods`	denotes a vector of the desired methods where "eQTL.linear" is a linear regression using an inverse normal transformation for the total number of read counts. "eQTL.negBin" is a negative binomial regression for the total number of read counts. "eQTL.quasipoisson" is a quasipoisson regression for the total number of read counts. "ASE.BetaBinom" is a beta binomial test for ASE. "eQTL.ASE" is an approach by Wei Sun that incorporates both eQTL and ASE analysis. (2012) A Statistical Framework for eQTL Mpping Using RNA-seq Data, Biometrics, 2012 Mar;68(1):1-11.
`folds`	denotes the fold change.
`alpha`	denotes the significance level.
`phi`	denotes the dispersion parameter for the negative binomial distribution for the total number of read counts.
`theta`	specifies the extent of ASE.
`maf`	denotes the minor allele frequency.
`propASE`	denotes the proportion of the total read count that is available for the allele specific read. The default based on real datasets is 0.005.
`legend`	is TRUE if you want the legend to be displayed for the graph or FALSE if you don't want the legend displayed on the graph.
`color`	is TRUE if you want the graph in color or FALSE if you want it in grayscale.
`title`	specifies the main title of the graph, default is none.
`subtitle`	specifies the subtitle of the graph, default is none
`titlecolor`	denotes what color the title will be
`subtitlecolor`	denotes what color the subtitle will be
`titlesize`	denotes what size the title will be, default is 1
`subtitlesize`	denotes what size the subtitle will be, default is 1
`labelsize`	denotes what size the axis labels will be, default is 1
`labelcolor`	denotes what color the axis labels will be
`linewidth`	denotes the boldness of the lines on the graph
`tilt`	denotes whether or not the y axis labels are tilted, default is 0, 1 will rotate labels 90 degrees
`SEED`	sets the seed, default = 1.