fsusie_log_plot: fSuSiE Plots using Gviz

In stephenslab/susiF.alpha: Sum of Single Functions

fSuSiE Plots using Gviz

Description

fSuSiE Plots using Gviz

Usage

fsusie_log_plot(
  obj,
  chr,
  pos0,
  pos1,
  X,
  Y,
  snp_info,
  cs = 1,
  log1p_count = FALSE,
  effect_log = TRUE,
  thresh_lfsr = NULL,
  data_splice = NULL,
  type_data = "p"
)

Arguments

obj	is the fsusie object
chr	the chromosome number
pos0	the start of the RNAseq count (genomic position of the first column of the Y matrix used to fit the fsusie object) description
pos1	the end of the RNAseq count (genomic position of the last column of the Y matrix used to fit the fsusie object) description
X	the X matrix used to fit fsusie
Y	the Y matrix used to fit fsusie
snp_info	'optional) a matrix containing the information of the genotype matrix see vignette on RNaseq
cs	the cs number to be plotted
log1p_count	logical (default to FALSE) show the observe count conditional on the leads SNP in the using log1p_count
effect_log	logical (set to TRUE) , the plot assume that you fitted the fsusie object on log +1 count and so if you set this parameter to FALSE the displayed effect will be the expected difference in count instead of the fitted curve
thresh_lfsr	if the susiF object is fitted using HMM postprocessing you can use this argument to set to 0 the estimated effect that have an local false sign rate higher than a given threshold (e.g., 0.05) description
type_data	set to "p" change the type of plot for the observed count conditional of the lead SNP see GViz documentation

stephenslab/susiF.alpha documentation built on June 11, 2025, 1:09 p.m.