import_AccINFO: Import Accession Information from File

In geneHapR: Gene Haplotype Statistics, Phenotype Association and Visualization

Import Accession Information from File

Description

import accession information including phenotype data, accession group, location from a tab delimed table file

Usage

import_AccINFO(file, comment.char = "#",
               check.names = FALSE, row.names = 1, ...)

Arguments

file	file path, this file should be a tab delimed table
comment.char	character: a character vector of length one containing a single character or an empty string. Use "" to turn off the interpretation of comments altogether.
check.names	logical. If TRUE then the names of the variables in the data frame are checked to ensure that they are syntactically valid variable names. If necessary they are adjusted (by make.names) so that they are, and also to ensure that there are no duplicates.
row.names	a vector of row names. This can be a vector giving the actual row names, or a single number giving the column of the table which contains the row names, or character string giving the name of the table column containing the row names. If there is a header and the first row contains one fewer field than the number of columns, the first column in the input is used for the row names. Otherwise if row.names is missing, the rows are numbered. Using row.names = NULL forces row numbering. Missing or NULL row.names generate row names that are considered to be ‘automatic’ (and not preserved by as.matrix).
...	Further arguments to be passed to read.table.

Details

First column should be Accessions; phenos/accession information should begin from second column, phenoName/group/locations should located at the first row, If a dot '.' is located in pheno name, then the part before the dot will be set as y axis name and the latter will be set as foot when plot figures.

Value

data.frame, Accession names were set as rownames and columns were named by pheno/info names

Examples

oldDir <- getwd()
temp_dir <- tempdir()
if(! dir.exists(temp_dir))
  dir.create(temp_dir)
setwd(temp_dir)
data("geneHapR_test")
write.table(pheno, file = "test.pheno.txt", sep = "\t")
pheno <- import_AccINFO("test.pheno.txt")
pheno
setwd(oldDir)

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