fSuSiE Plots using Gviz

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