solarius (version 0.3.0.2)

matchIdNames: Match ID column names

Description

The function automates the process of renaming ID fields in data frame of phenotypes into a SOLAR format.

Usage

matchIdNames(fields, sex.optional = FALSE, skip.sex = FALSE)

Arguments

fields

The name of fields or colulm names in data frame, which are candidates to be ID fields.

sex.optional

Logical, indicating if through an error in the case SEX field is not found in input fields.

skip.sex

Logical, indicating if the search for SEX filds is completely skipped.

Value

A named character vector, that can be directly passed to rename function of plyr package.

Examples

# @ http://helix.nih.gov/Documentation/solar-6.6.2-doc/91.appendix_1_text.html#load
#solar> help file-pedigree                                                       
#
# The pedigree file consists of one record for each individual in the data
# set.  Each record must include the following fields:
#
#    ego ID, father ID, mother ID, sex
#
# In addition, a family ID is required when ego IDs are not unique across
# the entire data set.  If the data set contains genetically identical
# individuals, an MZ-twin ID must be present (as described below).  If an
# analysis of household effects is planned, a household ID can be included
# (also described below).
#
# The default field names are ID, FA, MO, SEX, FAMID, MZTWIN, and HHID.
#

fields <- c("id", "ID", "ids",
  "famid", "FAMID", "famidity",
  "mo", "MO", "mother", "MOTHER", "MOtrait", "motherland",
  "fa", "FA", "father", "FATHER", "fatherland",
  "sex", "SEX", "sexo")

### ID
# pass: id, ID
# filter: ids
grep("^id$|^ID$", fields, value = TRUE)

### FAMID
grep("^famid$|^FAMID$", fields, value = TRUE)

### MO
grep("^mo$|^MO$|^mother$|^MOTHER$", fields, value = TRUE)

### FA
grep("^fa$|^FA$|^father$|^FATHER$", fields, value = TRUE)

### SEX
grep("^sex$|^SEX$", fields, value = TRUE)