hapVsPhenos: hapVsPhenos

In geneHapR: Gene Haplotype Statistics, Phenotype Association and Visualization

hapVsPhenos

Description

hapVsPhenos

Usage

hapVsPhenos(
  hap,
  pheno,
  outPutSingleFile = TRUE,
  hapPrefix = "H",
  title = "Seita.0G000000",
  width = 12,
  height = 8,
  res = 300,
  compression = "lzw",
  filename.prefix = filename.prefix,
  filename.surfix = "pdf",
  filename.sep = "_",
  outlier.rm = TRUE,
  mergeFigs = TRUE,
  ...
)

Arguments

hap	object of hapResult class, generate withvcf2hap() or seqs2hap()
pheno	object of data.frame class, imported by import_pheno()
outPutSingleFile	TRUE or FALSE indicate whether put all figs into to each pages of single file or generate multi-files. Only worked while file type is pdf
hapPrefix	prefix of hapotypes, default as "H"
title	a charater which will used for figure title
width	manual option for determining the output file width in inches. (default: 12)
height	manual option for determining the output file height in inches. (default: 8)
res	The nominal resolution in ppi which will be recorded in the bitmap file, if a positive integer. Also used for units other than the default, and to convert points to pixels
compression	the type of compression to be used.
filename.prefix, filename.surfix, filename.sep	if multi files generated, file names will be formed by prefix filename.prefix, a seperate charcter filename.sep, pheno name, a dot and surfix filename.surfix, and file type was decide by filename.surfix; if single file was generated, file name will be formed by prefix filename.prefix, a dot and surfix filename.surfix
outlier.rm	whether remove ouliers, default as TRUE
mergeFigs	bool type, indicate whether merge the heat map and box plot or not. Default as FALSE
...	Arguments passed on to hapVsPheno phenoName pheno name for plot, should be one column name of pheno minAcc,freq.min If observations number of a Hap less than this number will not be compared with others or be ploted. Should not less than 3 due to the t-test will meaninglessly. Default as 5 angle the angle of x labels hjust,vjust hjust and vjust of x labels comparisons a list contains comparison pairs eg. list(c("H001", "H002"), c("H001", "H004")), or a character vector contains haplotype names for comparison, or "none" indicates do not add comparisons. method a character string indicating which method to be used for comparing means. method.args a list of additional arguments used for the test method. For example one might use method.args = list(alternative = "greater") for wilcoxon test. symnum.args a list of arguments to pass to the function symnum for symbolic number coding of p-values. For example, symnum.args <- list(cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05, Inf), symbols = c("****", "***", "**", "*", "ns")). In other words, we use the following convention for symbols indicating statistical significance: ns: p > 0.05 *: p <= 0.05 **: p <= 0.01 ***: p <= 0.001 ****: p <= 0.0001

Value

No return value

Examples

data("geneHapR_test")

oriDir <- getwd()
temp_dir <- tempdir()
if(! dir.exists(temp_dir))
  dir.create(temp_dir)
setwd(temp_dir)
# analysis all pheno in the data.frame of pheno
hapVsPhenos(hapResult,
            pheno,
            outPutSingleFile = TRUE,
            hapPrefix = "H",
            title = "Seita.0G000000",
            filename.prefix = "test",
            width = 12,
            height = 8,
            res = 300)
setwd(oriDir)

geneHapR documentation built on May 29, 2024, 11:59 a.m.