R/simpleTests.R
In IngaPa/myDNA: myDNA: R package to analyze personal genotypes
Defines functions
lactoseIntolerance
celiacDisease23AndMe
celiacDiseaseExtended
cofeeConsumption
deepSleeper
muscleComposition
bitterPTCTaster
blueEyes
blueEyesExtended
neanderthalMe
redHair
Documented in
bitterPTCTaster
blueEyes
blueEyesExtended
celiacDisease23AndMe
celiacDiseaseExtended
cofeeConsumption
deepSleeper
lactoseIntolerance
muscleComposition
neanderthalMe
redHair
##########################################
# --- screen for lactose intolerance ----
##########################################
#' Function to screen for lactose intolerance
#'
#' @param myDNA (character) path to the genotype file
#'
#' @details SOURCE: 23andMe report
#' INFO:
#' Lactose intolerance is influenced by a genetic marker near the LCT gene.
#' GG - likely lactose intolerant. CG/CC - likely not lactose intolerant
#'
#' !!!! myAllele column reports whether risk allele was identified in my genome
#'
#' @import stringr
#'
#' @examples
#'
#' \dontrun{
#' # example myHeritage
# library(myDNA)
# library(dplyr)
# library(stringr)
# Genome="/data/akalin/Projects/AAkalin_myDNA/Data/MyHeritage/MyHeritage_raw_dna_dataInga/MyHeritage_raw_dna_data.csv"
# myDNA <- importDNA(myGenotypes = Genome,type = "myHeritage" )
# lactoseIntolerance(myDNA)
#' }
#' @author Inga Patarcic
#' @export
lactoseIntolerance <- function(myDNA) {
SCREEN <- (myDNAScreenSNPS(myDNA = myDNA,
snpsData = cbind("rs4988235","G")))
if (nrow(SCREEN)==0) {
stop("SNP not present in the genotype data, try with imputed dataset")}
if (nrow(SCREEN)!=0) {return(SCREEN)}
}
###########################################
# --- screen for celiac disease ---
###########################################
#' Function to screen for celiac disease based on 23andMe tested SNPs
#'
#' @param myDNA (character) path to the genotype file
#'
#' @details
#' SCREEN 1: rs2187668 (T) and rs7454108 (G)
#' SOURCE: https://blog.23andme.com/health-traits/new-23andme-report-celiac-disease/
#'
#' NOTE! MyHeritage genotypes do not report this SNP, however missing genotypes
#' can be imputed and accessed by DNALand imputation tool
#'
#' !!!! myAllele column reports whether risk allele was identified in my genome
#'
#' @import stringr
#'
#' @examples \dontrun{
#' # example myHeritage
#' library(myDNA)
#' library(dplyr)
#' library(stringr)
#' Genome="/data/akalin/Projects/AAkalin_myDNA/Data/MyHeritage/MyHeritage_raw_dna_dataInga/MyHeritage_raw_dna_data.csv"
#' myDNA <- importDNA(myGenotypes = Genome,type = "myHeritage" )
#' celiacDisease23AndMe(myDNA)
#' }
#' @author Inga Patarcic
#' @export
celiacDisease23AndMe <- function(myDNA) {
SCREEN <- (myDNAScreenSNPS(myDNA = myDNA,
snpsData = cbind(c("rs2187668",
"rs7454108"),
c("T","G"))))
if (nrow(SCREEN)==0) {
stop("SNP not present in the genotype data, try with imputed dataset")}
if (nrow(SCREEN)!=0) {return(SCREEN)}
}
#' Function to screen for celiac disease based on 6 CD associated SNPs
#'
#' @param myDNA (character) path to the genotype file
#'
#' @details
#' SOURCE: https://www.mygenefood.com/genetics-celiac-disease-need-know/
#' https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386975/
#' DQ2.5 rs2187668 T (0.09)
#' DQ8 rs7454108 G (0.18)
#' DQ2.2 rs2395182 T (0.71)
#' rs7775228 G (0.10)
#' rs4713586 G (0.025)
#' DQ7 rs4639334 A (0.09)
#' NOTE! MyHeritage genotypes do not report this SNP, however missing genotypes
#' can be imputed and accessed by DNALand imputation tool
#'
#' !!!! myAllele column reports whether risk allele was identified in my genome
#'
#' @import stringr
#'
#' @examples \dontrun{
#' # example myHeritage
#' library(myDNA)
#' library(dplyr)
#' library(stringr)
#' Genome="/data/akalin/Projects/AAkalin_myDNA/Data/MyHeritage/MyHeritage_raw_dna_dataInga/MyHeritage_raw_dna_data.csv"
#' myDNA <- importDNA(myGenotypes = Genome,type = "myHeritage" )
#' celiacDiseaseExtended(myDNA)
#' }
#' @author Inga Patarcic
#' @export
celiacDiseaseExtended <- function(myDNA){
SCREEN <- (myDNAScreenSNPS(myDNA = myDNA,
snpsData = cbind(c("rs2395182",
"rs7775228",
"rs4713586",
"rs2187668",
"rs4639334" ,
"rs7454108"),
c("T","G","G","T","A","G"))))
if (nrow(SCREEN)==0) {
stop("SNP not present in the genotype data, try with imputed dataset")}
if (nrow(SCREEN)!=0) {return(SCREEN)}
}
###########################################
# --- screen for coffee consumption ---
###########################################
#' Function to screen for higher coffee consumption
#'
#' @param myDNA (character) path to the genotype file
#'
#' @details
#' SOURCE: 23andMe report
#' INFO:
#' Report is based on genetic variants near two genes that play a role in how
#' your body handles caffeine. The first gene, CYP1A2, contains instructions for
#' an enzyme that breaks down 95% of the caffeine you consume.
#' The second gene, AHR (rs4410790), contains instructions for a protein that ramps
#' up production of the CYP1A2 enzyme. Variants in these genes may affect
#' how quickly the body breaks down and clears away caffeine.
#' NOTE! MyHeritage genotypes do not report this SNP, however missing genotypes
#' can be imputed and accessed by DNALand imputation tool
#' The CYP1A2 gene (rs2472297) contains instructions for an enzyme that breaks
#' down many substances, including caffeine.
#' This enzyme is a member of a large family of enzymes called cytochrome P450.
#' Presence of variants: likely higher coffee consumption.
#'
#' !!!! myAllele column reports whether risk allele was identified in my genome
#'
#' @import stringr
#'
#' @examples
#'
#' \dontrun{
#' # example myHeritage
#' library(myDNA)
#' library(dplyr)
#' library(stringr)
#' Genome="/data/akalin/Projects/AAkalin_myDNA/Data/MyHeritage/MyHeritage_raw_dna_dataInga/MyHeritage_raw_dna_data.csv"
#' myDNA <- importDNA(myGenotypes = Genome,type = "myHeritage" )
#' cofeeConsumption(myDNA)
#' }
#' @author Inga Patarcic
#' @export
cofeeConsumption <- function(myDNA){
SCREEN <- (myDNAScreenSNPS(myDNA = myDNA,
snpsData = cbind(c("rs2472297",
"rs4410790"),
c("T","C"))))
if (nrow(SCREEN)==0) {
stop("SNP not present in the genotype data, try with imputed dataset")}
if (nrow(SCREEN)!=0) {return(SCREEN)}
}
###########################################
# --- screen for deep sleep ---
###########################################
#' Function to screen for deep sleep
#'
#' @param myDNA (character) path to the genotype file
#'
#' @details
#' SOURCE: 23andMe report
#' INFO from 23andMe:
#' The genetic marker in this report is in the ADA gene,
#' which contains instructions for an enzyme that helps control adenosine levels.
#' Scientists think that adenosine builds up more quickly in people with one or
#' two copies of the T variant at this marker. This extra adenosine increases
#' sleepiness, leading to stronger delta waves. Because of this stronger sleep
#' pressure, people with the T variant also report feeling sleepier than other
#' people after a night of missed sleep.
#'
#'
#' NOTE! MyHeritage genotypes do not report this SNP, however missing genotypes
#' can be imputed and accessed by DNALand imputation tool
#'
#' !!!! myAllele column reports whether risk allele was identified in my genome
#'
#' @import stringr
#'
#' @examples
#'
#' \dontrun{
#' # example myHeritage
#' library(myDNA)
#' library(dplyr)
#' library(stringr)
#' Genome="/data/akalin/Projects/AAkalin_myDNA/Data/MyHeritage/MyHeritage_raw_dna_dataInga/MyHeritage_raw_dna_data.csv"
#' myDNA <- importDNA(myGenotypes = Genome,type = "myHeritage" )
#' deepSleeper(myDNA)
#' }
#' @author Inga Patarcic
#' @export
deepSleeper <- function(myDNA){
SCREEN <- (myDNAScreenSNPS(myDNA = myDNA,
snpsData = cbind("rs73598374","T")))
if (nrow(SCREEN)==0) {
stop("SNP not present in the genotype data, try with imputed dataset")}
if (nrow(SCREEN)!=0) {return(SCREEN)}
}
###########################################
# --- screen for Muscle Composition ---
###########################################
#' Function to screen for production of ACTN3 gene
#'
#'
#' @param myDNA (character) path to the genotype file
#'
#' @details
#' SOURCE: 23andMe report
#' INFO:
#' A genetic marker in the ACTN3 gene.
#' This marker controls whether muscle cells produce a protein
#' (called alpha-actinin-3) that's found in fast-twitch muscle fibers.
#' While some people don't produce this protein at all, almost all of the elite
#' power athletes who have been studied have a genetic variant that allows them to
#' produce the protein. This suggests that the protein may be beneficial at least
#' at the highest levels of power-based athletic competition.
#'
#' NOTE! MyHeritage genotypes do not report this SNP, however missing genotypes
#' can be imputed and accessed by DNALand imputation tool
#'
#' !!!! myAllele column reports whether risk allele was identified in my genome
#'
#' @import stringr
#'
#' @examples
#'
#' \dontrun{
#' # example myHeritage
#' library(myDNA)
#' library(dplyr)
#' library(stringr)
#' Genome="/data/akalin/Projects/AAkalin_myDNA/Data/MyHeritage/MyHeritage_raw_dna_dataInga/MyHeritage_raw_dna_data.csv"
#' myDNA <- importDNA(myGenotypes = Genome,type = "myHeritage" )
#' muscleComposition(myDNA)
#' }
#' @author Inga Patarcic
#' @export
muscleComposition <- function(myDNA){
SCREEN <- (myDNAScreenSNPS(myDNA = myDNA,
snpsData = cbind("rs1815739","C")))
if (nrow(SCREEN)==0) {
stop("SNP not present in the genotype data, try with imputed dataset")}
if (nrow(SCREEN)!=0) {return(SCREEN)}
}
###########################################
# --- screen for PTC bitter taste ---
###########################################
#' Function to screen for PTC bitter tasting ability
#'
#'
#' @param myDNA (character) path to the genotype file
#'
#' @details
#' SOURCE: 23andMe report
#'
#' INFO:
#' rs713598 - a genetic marker that affects your chances of being able to detect
#' a certain bitter chemical called "PTC." Some vegetables like raw broccoli
#' and brussels sprouts, contain bitter chemicals similar to PTC.
#' CC - unable to detect, GG/CG - able to detect.
#' The TAS2R38 gene contains instructions for a protein, or taste receptor,
#' that can detect the bitter chemical called "PTC."
#'
#' NOTE! MyHeritage genotypes do not report this SNP, however missing genotypes
#' can be imputed and accessed by DNALand imputation tool
#'
#' !!!! myAllele column reports whether risk allele was identified in my genome
#'
#'
#' @import stringr
#'
#' @examples
#'
#' \dontrun{
#' # example myHeritage
#' library(myDNA)
#' library(dplyr)
#' library(stringr)
#' Genome="/data/akalin/Projects/AAkalin_myDNA/Data/MyHeritage/MyHeritage_raw_dna_dataInga/MyHeritage_raw_dna_data.csv"
#' myDNA <- importDNA(myGenotypes = Genome,type = "myHeritage" )
#' bitterPTCTaster(myDNA)
#' }
#' @author Inga Patarcic
#' @export
bitterPTCTaster <- function(myDNA) {
SCREEN <- (myDNAScreenSNPS(myDNA = myDNA,
snpsData = cbind("rs713598","G")))
if (nrow(SCREEN)==0) {
stop("SNP not present in the genotype data, try with imputed dataset")}
if (nrow(SCREEN)!=0) {return(SCREEN)}
}
###########################################
# --- screen for blue eyes ---
###########################################
#' Function to screen for production of ACTN3 gene
#'
#'
#' @param myDNA (character) path to the genotype file
#'
#' @details
#' SOURCE 1: 23andMe report
#' INFO:
#' The genetic marker in this report is located near a gene called OCA2 that
#' affects how much brown pigment your cells produce. People with 1 or 2 copies
#' of the A variant of this marker tend to have more brown pigment in their eyes,
#' so they are likely to have darker eyes.
#' AA/AG - likely brown/hazel eyes, GG - likely blue/green eyes
#' NOTE! MyHeritage genotypes do not report this SNP, however missing genotypes
#' can be imputed and accessed by DNALand imputation tool
#'
#' !!!! myAllele column reports whether risk allele was identified in my genome
#'
#' @import stringr
#'
#' @examples
#'
#' \dontrun{
#' # example myHeritage
#' library(myDNA)
#' library(dplyr)
#' library(stringr)
#' Genome="/data/akalin/Projects/AAkalin_myDNA/Data/MyHeritage/MyHeritage_raw_dna_dataInga/MyHeritage_raw_dna_data.csv"
#' myDNA <- importDNA(myGenotypes = Genome,type = "myHeritage" )
#' blueEyes(myDNA)
#' }
#' @author Inga Patarcic
#' @export
blueEyes <- function(myDNA) {
SCREEN <- myDNAScreenSNPS(myDNA = myDNA,
snpsData = cbind("rs12913832","G"))
if (nrow(SCREEN)==0) {
stop("SNP not present in the genotype data, try with imputed dataset")}
if (nrow(SCREEN)!=0) {return(SCREEN)}
}
#' Function to screen for testing eye color
#'
#'
#' @param myDNA (character) path to the genotype file
#'
#' @details
#' Source 2: SNPedia for rs12913832
#' resuts source 2: rs12913832 is also part of a haplotype spanning
#' 166kB on chromosome 15, defined by 13 SNPs listed below,
#' that is found in 97% of all Caucasians with blue eyes.
#' The "h-1" haplotype found in homozygous state in 97% of individuals
#' with blue eye color is composed as follows [PMID 18172690]:
#'
#' rs4778241(C)
#' rs1129038(A)
#' rs12593929(A)
#' rs12913832(G) OCA2/HERC2 has a score of 51.5 and an estimated allelic OR of 8.43
#' rs7183877(C)
#' rs3935591(G)
#' rs7170852(A)
#' rs2238289(T)
#' rs3940272(C)
#' rs8028689(T)
#' rs2240203(A)
#' rs11631797(G)
#' rs916977(G)
#' ADDED from SNPedia: rs1667394 increases susceptibility to Blond rather than
#' brown hair 4.94 times for carriers of the A allele
#'
#' !!!! myAllele column reports whether risk allele was identified in my genome
#'
#' @import stringr
#'
#' @examples
#'
#' \dontrun{
#' # example myHeritage
#' library(myDNA)
#' library(dplyr)
#' library(stringr)
#' Genome="/data/akalin/Projects/AAkalin_myDNA/Data/MyHeritage/MyHeritage_raw_dna_dataInga/MyHeritage_raw_dna_data.csv"
#' myDNA <- importDNA(myGenotypes = Genome,type = "myHeritage" )
#' blueEyesExtended(myDNA)
#' }
#' @author Inga Patarcic
#' @export
blueEyesExtended <- function(myDNA) {
SCREEN <- myDNAScreenSNPS(myDNA = myDNA,
snpsData = cbind(c("rs1667394","rs4778241",
"rs1129038",
"rs12593929",
"rs12913832",
"rs7183877",
"rs3935591",
"rs7170852",
"rs2238289",
"rs3940272",
"rs8028689",
"rs2240203",
"rs11631797",
"rs916977"),
c("A","C","A","A","G","C","G","A","T","C","T","A","G","G")))
if (nrow(SCREEN)==0) {
stop("SNP not present in the genotype data, try with imputed dataset")}
if (nrow(SCREEN)!=0) {return(SCREEN)}
}
###########################################
# --- screen for Neanderthal SNPs ---
###########################################
#' Function to screen for certain Neanderthal variants
#'
#'
#' @param myDNA (character) path to the genotype file
#'
#' @details
#' SOURCE 1: 23andMe report
#' If you have certain Neanderthal variants, it means that some of your physical
#' traits may trace back to your Neanderthal ancestors.
#'
#' Tested variants/gene/trait:
#' rs7544462/Gene: MEAF6/Trait: Height
#' rs1877547/Gene: LPP/Trait: Height
#' rs4849721/Gene: Near the EN1 gene/Trait: Less back hair
#' rs12458349/Gene: Near the PHLPP1 gene/Trait: Straight hair
#' rs11213819/Gene: Near the C11orf53 gene/Trait: Less likely to
#' sneeze after eating dark chocolate
#'
#' NOTE! MyHeritage genotypes do not report some if the SNPs, however missing
#' genotypes can be imputed and accessed by DNALand imputation tool
#'
#' !!!! myAllele column reports whether risk allele was identified in my genome
#'
#' @import stringr
#'
#' @examples
#'
#' \dontrun{
#' # example myHeritage
#' library(myDNA)
#' library(dplyr)
#' library(stringr)
#' Genome="/data/akalin/Projects/AAkalin_myDNA/Data/MyHeritage/MyHeritage_raw_dna_dataInga/MyHeritage_raw_dna_data.csv"
#' myDNA <- importDNA(myGenotypes = Genome,type = "myHeritage" )
#' neanderthalMe(myDNA)
#' }
#' @author Inga Patarcic
#' @export
neanderthalMe <- function(myDNA) {
SCREEN <- myDNAScreenSNPS(myDNA = myDNA,
snpsData = cbind(c("rs7544462",
"rs1877547",
"rs4849721",
"rs12458349",
"rs11213819"),
c("C","A","T","G","T")))
if (nrow(SCREEN)==0) {
stop("SNP not present in the genotype data, try with imputed dataset")}
if (nrow(SCREEN)!=0) {return(SCREEN)}
}
###########################################
# --- screen for red hair ---
###########################################
#' Function to screen for red hairiness
#'
#'
#' @param myDNA (character) path to the genotype file
#'
#' @details
#' SOURCE 1: 23andMe report
#' NOTE! MyHeritage genotypes do not report some if the SNPs, however missing
#' genotypes can be imputed and accessed by DNALand imputation tool
#' INFO:
#' Several variants in a single gene, MC1R, can cause red hair by increasing
#' the amount of pheomelanin in your hair.
#' Hair color is determined by not just how much pigment you have,
#' but also what kind. Whether you have red hair depends on your levels of
#' red/yellow pigment (pheomelanin). But the lightness or darkness of your hair
#' depends on your levels of a brown/black pigment called eumelanin
#' REPORTED SNPS: rs1805007,rs1805008,i3002507
#'
#' SOURCE 2: https://www.snpedia.com/index.php/I3002507
#' i3002507 alias rs1805009 identified in SNPedia
#' proxy calculations needed
#'
#' !!!! myAllele column reports whether risk allele was identified in my genome
#'
#' @import stringr
#'
#' @examples
#'
#' \dontrun{
#' # example myHeritage
#' library(myDNA)
#' library(dplyr)
#' library(stringr)
#' Genome="/data/akalin/Projects/AAkalin_myDNA/Data/MyHeritage/MyHeritage_raw_dna_dataInga/MyHeritage_raw_dna_data.csv"
#' myDNA <- importDNA(myGenotypes = Genome,type = "myHeritage" )
#' redHair(myDNA)
#' }
#' @author Inga Patarcic
#' @export
redHair <- function(myDNA) {
SCREEN <- suppressWarnings(myDNAScreenSNPS(myDNA = myDNA,
snpsData = cbind(c("rs1805007",
"rs1805008",
"rs1805009"),
c("T","T","C"))))
if (nrow(SCREEN)==0) {
stop("SNP not present in the genotype data, try with imputed dataset")}
if (nrow(SCREEN)!=0) {return(SCREEN)}
}
IngaPa/myDNA documentation built on Oct. 30, 2019, 7:22 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions lactoseIntolerance celiacDisease23AndMe celiacDiseaseExtended cofeeConsumption deepSleeper muscleComposition bitterPTCTaster blueEyes blueEyesExtended neanderthalMe redHair
Documented in bitterPTCTaster blueEyes blueEyesExtended celiacDisease23AndMe celiacDiseaseExtended cofeeConsumption deepSleeper lactoseIntolerance muscleComposition neanderthalMe redHair
##########################################
# --- screen for lactose intolerance ----
##########################################
#' Function to screen for lactose intolerance
#'
#' @param myDNA (character) path to the genotype file
#'
#' @details SOURCE: 23andMe report
#' INFO:
#' Lactose intolerance is influenced by a genetic marker near the LCT gene.
#' GG - likely lactose intolerant. CG/CC - likely not lactose intolerant
#'
#' !!!! myAllele column reports whether risk allele was identified in my genome
#'
#' @import stringr
#'
#' @examples
#'
#' \dontrun{
#' # example myHeritage
# library(myDNA)
# library(dplyr)
# library(stringr)
# Genome="/data/akalin/Projects/AAkalin_myDNA/Data/MyHeritage/MyHeritage_raw_dna_dataInga/MyHeritage_raw_dna_data.csv"
# myDNA <- importDNA(myGenotypes = Genome,type = "myHeritage" )
# lactoseIntolerance(myDNA)
#' }
#' @author Inga Patarcic
#' @export
lactoseIntolerance <- function(myDNA) {
SCREEN <- (myDNAScreenSNPS(myDNA = myDNA,
snpsData = cbind("rs4988235","G")))
if (nrow(SCREEN)==0) {
stop("SNP not present in the genotype data, try with imputed dataset")}
if (nrow(SCREEN)!=0) {return(SCREEN)}
}
###########################################
# --- screen for celiac disease ---
###########################################
#' Function to screen for celiac disease based on 23andMe tested SNPs
#'
#' @param myDNA (character) path to the genotype file
#'
#' @details
#' SCREEN 1: rs2187668 (T) and rs7454108 (G)
#' SOURCE: https://blog.23andme.com/health-traits/new-23andme-report-celiac-disease/
#'
#' NOTE! MyHeritage genotypes do not report this SNP, however missing genotypes
#' can be imputed and accessed by DNALand imputation tool
#'
#' !!!! myAllele column reports whether risk allele was identified in my genome
#'
#' @import stringr
#'
#' @examples \dontrun{
#' # example myHeritage
#' library(myDNA)
#' library(dplyr)
#' library(stringr)
#' Genome="/data/akalin/Projects/AAkalin_myDNA/Data/MyHeritage/MyHeritage_raw_dna_dataInga/MyHeritage_raw_dna_data.csv"
#' myDNA <- importDNA(myGenotypes = Genome,type = "myHeritage" )
#' celiacDisease23AndMe(myDNA)
#' }
#' @author Inga Patarcic
#' @export
celiacDisease23AndMe <- function(myDNA) {
SCREEN <- (myDNAScreenSNPS(myDNA = myDNA,
snpsData = cbind(c("rs2187668",
"rs7454108"),
c("T","G"))))
if (nrow(SCREEN)==0) {
stop("SNP not present in the genotype data, try with imputed dataset")}
if (nrow(SCREEN)!=0) {return(SCREEN)}
}
#' Function to screen for celiac disease based on 6 CD associated SNPs
#'
#' @param myDNA (character) path to the genotype file
#'
#' @details
#' SOURCE: https://www.mygenefood.com/genetics-celiac-disease-need-know/
#' https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386975/
#' DQ2.5 rs2187668 T (0.09)
#' DQ8 rs7454108 G (0.18)
#' DQ2.2 rs2395182 T (0.71)
#' rs7775228 G (0.10)
#' rs4713586 G (0.025)
#' DQ7 rs4639334 A (0.09)
#' NOTE! MyHeritage genotypes do not report this SNP, however missing genotypes
#' can be imputed and accessed by DNALand imputation tool
#'
#' !!!! myAllele column reports whether risk allele was identified in my genome
#'
#' @import stringr
#'
#' @examples \dontrun{
#' # example myHeritage
#' library(myDNA)
#' library(dplyr)
#' library(stringr)
#' Genome="/data/akalin/Projects/AAkalin_myDNA/Data/MyHeritage/MyHeritage_raw_dna_dataInga/MyHeritage_raw_dna_data.csv"
#' myDNA <- importDNA(myGenotypes = Genome,type = "myHeritage" )
#' celiacDiseaseExtended(myDNA)
#' }
#' @author Inga Patarcic
#' @export
celiacDiseaseExtended <- function(myDNA){
SCREEN <- (myDNAScreenSNPS(myDNA = myDNA,
snpsData = cbind(c("rs2395182",
"rs7775228",
"rs4713586",
"rs2187668",
"rs4639334" ,
"rs7454108"),
c("T","G","G","T","A","G"))))
if (nrow(SCREEN)==0) {
stop("SNP not present in the genotype data, try with imputed dataset")}
if (nrow(SCREEN)!=0) {return(SCREEN)}
}
###########################################
# --- screen for coffee consumption ---
###########################################
#' Function to screen for higher coffee consumption
#'
#' @param myDNA (character) path to the genotype file
#'
#' @details
#' SOURCE: 23andMe report
#' INFO:
#' Report is based on genetic variants near two genes that play a role in how
#' your body handles caffeine. The first gene, CYP1A2, contains instructions for
#' an enzyme that breaks down 95% of the caffeine you consume.
#' The second gene, AHR (rs4410790), contains instructions for a protein that ramps
#' up production of the CYP1A2 enzyme. Variants in these genes may affect
#' how quickly the body breaks down and clears away caffeine.
#' NOTE! MyHeritage genotypes do not report this SNP, however missing genotypes
#' can be imputed and accessed by DNALand imputation tool
#' The CYP1A2 gene (rs2472297) contains instructions for an enzyme that breaks
#' down many substances, including caffeine.
#' This enzyme is a member of a large family of enzymes called cytochrome P450.
#' Presence of variants: likely higher coffee consumption.
#'
#' !!!! myAllele column reports whether risk allele was identified in my genome
#'
#' @import stringr
#'
#' @examples
#'
#' \dontrun{
#' # example myHeritage
#' library(myDNA)
#' library(dplyr)
#' library(stringr)
#' Genome="/data/akalin/Projects/AAkalin_myDNA/Data/MyHeritage/MyHeritage_raw_dna_dataInga/MyHeritage_raw_dna_data.csv"
#' myDNA <- importDNA(myGenotypes = Genome,type = "myHeritage" )
#' cofeeConsumption(myDNA)
#' }
#' @author Inga Patarcic
#' @export
cofeeConsumption <- function(myDNA){
SCREEN <- (myDNAScreenSNPS(myDNA = myDNA,
snpsData = cbind(c("rs2472297",
"rs4410790"),
c("T","C"))))
if (nrow(SCREEN)==0) {
stop("SNP not present in the genotype data, try with imputed dataset")}
if (nrow(SCREEN)!=0) {return(SCREEN)}
}
###########################################
# --- screen for deep sleep ---
###########################################
#' Function to screen for deep sleep
#'
#' @param myDNA (character) path to the genotype file
#'
#' @details
#' SOURCE: 23andMe report
#' INFO from 23andMe:
#' The genetic marker in this report is in the ADA gene,
#' which contains instructions for an enzyme that helps control adenosine levels.
#' Scientists think that adenosine builds up more quickly in people with one or
#' two copies of the T variant at this marker. This extra adenosine increases
#' sleepiness, leading to stronger delta waves. Because of this stronger sleep
#' pressure, people with the T variant also report feeling sleepier than other
#' people after a night of missed sleep.
#'
#'
#' NOTE! MyHeritage genotypes do not report this SNP, however missing genotypes
#' can be imputed and accessed by DNALand imputation tool
#'
#' !!!! myAllele column reports whether risk allele was identified in my genome
#'
#' @import stringr
#'
#' @examples
#'
#' \dontrun{
#' # example myHeritage
#' library(myDNA)
#' library(dplyr)
#' library(stringr)
#' Genome="/data/akalin/Projects/AAkalin_myDNA/Data/MyHeritage/MyHeritage_raw_dna_dataInga/MyHeritage_raw_dna_data.csv"
#' myDNA <- importDNA(myGenotypes = Genome,type = "myHeritage" )
#' deepSleeper(myDNA)
#' }
#' @author Inga Patarcic
#' @export
deepSleeper <- function(myDNA){
SCREEN <- (myDNAScreenSNPS(myDNA = myDNA,
snpsData = cbind("rs73598374","T")))
if (nrow(SCREEN)==0) {
stop("SNP not present in the genotype data, try with imputed dataset")}
if (nrow(SCREEN)!=0) {return(SCREEN)}
}
###########################################
# --- screen for Muscle Composition ---
###########################################
#' Function to screen for production of ACTN3 gene
#'
#'
#' @param myDNA (character) path to the genotype file
#'
#' @details
#' SOURCE: 23andMe report
#' INFO:
#' A genetic marker in the ACTN3 gene.
#' This marker controls whether muscle cells produce a protein
#' (called alpha-actinin-3) that's found in fast-twitch muscle fibers.
#' While some people don't produce this protein at all, almost all of the elite
#' power athletes who have been studied have a genetic variant that allows them to
#' produce the protein. This suggests that the protein may be beneficial at least
#' at the highest levels of power-based athletic competition.
#'
#' NOTE! MyHeritage genotypes do not report this SNP, however missing genotypes
#' can be imputed and accessed by DNALand imputation tool
#'
#' !!!! myAllele column reports whether risk allele was identified in my genome
#'
#' @import stringr
#'
#' @examples
#'
#' \dontrun{
#' # example myHeritage
#' library(myDNA)
#' library(dplyr)
#' library(stringr)
#' Genome="/data/akalin/Projects/AAkalin_myDNA/Data/MyHeritage/MyHeritage_raw_dna_dataInga/MyHeritage_raw_dna_data.csv"
#' myDNA <- importDNA(myGenotypes = Genome,type = "myHeritage" )
#' muscleComposition(myDNA)
#' }
#' @author Inga Patarcic
#' @export
muscleComposition <- function(myDNA){
SCREEN <- (myDNAScreenSNPS(myDNA = myDNA,
snpsData = cbind("rs1815739","C")))
if (nrow(SCREEN)==0) {
stop("SNP not present in the genotype data, try with imputed dataset")}
if (nrow(SCREEN)!=0) {return(SCREEN)}
}
###########################################
# --- screen for PTC bitter taste ---
###########################################
#' Function to screen for PTC bitter tasting ability
#'
#'
#' @param myDNA (character) path to the genotype file
#'
#' @details
#' SOURCE: 23andMe report
#'
#' INFO:
#' rs713598 - a genetic marker that affects your chances of being able to detect
#' a certain bitter chemical called "PTC." Some vegetables like raw broccoli
#' and brussels sprouts, contain bitter chemicals similar to PTC.
#' CC - unable to detect, GG/CG - able to detect.
#' The TAS2R38 gene contains instructions for a protein, or taste receptor,
#' that can detect the bitter chemical called "PTC."
#'
#' NOTE! MyHeritage genotypes do not report this SNP, however missing genotypes
#' can be imputed and accessed by DNALand imputation tool
#'
#' !!!! myAllele column reports whether risk allele was identified in my genome
#'
#'
#' @import stringr
#'
#' @examples
#'
#' \dontrun{
#' # example myHeritage
#' library(myDNA)
#' library(dplyr)
#' library(stringr)
#' Genome="/data/akalin/Projects/AAkalin_myDNA/Data/MyHeritage/MyHeritage_raw_dna_dataInga/MyHeritage_raw_dna_data.csv"
#' myDNA <- importDNA(myGenotypes = Genome,type = "myHeritage" )
#' bitterPTCTaster(myDNA)
#' }
#' @author Inga Patarcic
#' @export
bitterPTCTaster <- function(myDNA) {
SCREEN <- (myDNAScreenSNPS(myDNA = myDNA,
snpsData = cbind("rs713598","G")))
if (nrow(SCREEN)==0) {
stop("SNP not present in the genotype data, try with imputed dataset")}
if (nrow(SCREEN)!=0) {return(SCREEN)}
}
###########################################
# --- screen for blue eyes ---
###########################################
#' Function to screen for production of ACTN3 gene
#'
#'
#' @param myDNA (character) path to the genotype file
#'
#' @details
#' SOURCE 1: 23andMe report
#' INFO:
#' The genetic marker in this report is located near a gene called OCA2 that
#' affects how much brown pigment your cells produce. People with 1 or 2 copies
#' of the A variant of this marker tend to have more brown pigment in their eyes,
#' so they are likely to have darker eyes.
#' AA/AG - likely brown/hazel eyes, GG - likely blue/green eyes
#' NOTE! MyHeritage genotypes do not report this SNP, however missing genotypes
#' can be imputed and accessed by DNALand imputation tool
#'
#' !!!! myAllele column reports whether risk allele was identified in my genome
#'
#' @import stringr
#'
#' @examples
#'
#' \dontrun{
#' # example myHeritage
#' library(myDNA)
#' library(dplyr)
#' library(stringr)
#' Genome="/data/akalin/Projects/AAkalin_myDNA/Data/MyHeritage/MyHeritage_raw_dna_dataInga/MyHeritage_raw_dna_data.csv"
#' myDNA <- importDNA(myGenotypes = Genome,type = "myHeritage" )
#' blueEyes(myDNA)
#' }
#' @author Inga Patarcic
#' @export
blueEyes <- function(myDNA) {
SCREEN <- myDNAScreenSNPS(myDNA = myDNA,
snpsData = cbind("rs12913832","G"))
if (nrow(SCREEN)==0) {
stop("SNP not present in the genotype data, try with imputed dataset")}
if (nrow(SCREEN)!=0) {return(SCREEN)}
}
#' Function to screen for testing eye color
#'
#'
#' @param myDNA (character) path to the genotype file
#'
#' @details
#' Source 2: SNPedia for rs12913832
#' resuts source 2: rs12913832 is also part of a haplotype spanning
#' 166kB on chromosome 15, defined by 13 SNPs listed below,
#' that is found in 97% of all Caucasians with blue eyes.
#' The "h-1" haplotype found in homozygous state in 97% of individuals
#' with blue eye color is composed as follows [PMID 18172690]:
#'
#' rs4778241(C)
#' rs1129038(A)
#' rs12593929(A)
#' rs12913832(G) OCA2/HERC2 has a score of 51.5 and an estimated allelic OR of 8.43
#' rs7183877(C)
#' rs3935591(G)
#' rs7170852(A)
#' rs2238289(T)
#' rs3940272(C)
#' rs8028689(T)
#' rs2240203(A)
#' rs11631797(G)
#' rs916977(G)
#' ADDED from SNPedia: rs1667394 increases susceptibility to Blond rather than
#' brown hair 4.94 times for carriers of the A allele
#'
#' !!!! myAllele column reports whether risk allele was identified in my genome
#'
#' @import stringr
#'
#' @examples
#'
#' \dontrun{
#' # example myHeritage
#' library(myDNA)
#' library(dplyr)
#' library(stringr)
#' Genome="/data/akalin/Projects/AAkalin_myDNA/Data/MyHeritage/MyHeritage_raw_dna_dataInga/MyHeritage_raw_dna_data.csv"
#' myDNA <- importDNA(myGenotypes = Genome,type = "myHeritage" )
#' blueEyesExtended(myDNA)
#' }
#' @author Inga Patarcic
#' @export
blueEyesExtended <- function(myDNA) {
SCREEN <- myDNAScreenSNPS(myDNA = myDNA,
snpsData = cbind(c("rs1667394","rs4778241",
"rs1129038",
"rs12593929",
"rs12913832",
"rs7183877",
"rs3935591",
"rs7170852",
"rs2238289",
"rs3940272",
"rs8028689",
"rs2240203",
"rs11631797",
"rs916977"),
c("A","C","A","A","G","C","G","A","T","C","T","A","G","G")))
if (nrow(SCREEN)==0) {
stop("SNP not present in the genotype data, try with imputed dataset")}
if (nrow(SCREEN)!=0) {return(SCREEN)}
}
###########################################
# --- screen for Neanderthal SNPs ---
###########################################
#' Function to screen for certain Neanderthal variants
#'
#'
#' @param myDNA (character) path to the genotype file
#'
#' @details
#' SOURCE 1: 23andMe report
#' If you have certain Neanderthal variants, it means that some of your physical
#' traits may trace back to your Neanderthal ancestors.
#'
#' Tested variants/gene/trait:
#' rs7544462/Gene: MEAF6/Trait: Height
#' rs1877547/Gene: LPP/Trait: Height
#' rs4849721/Gene: Near the EN1 gene/Trait: Less back hair
#' rs12458349/Gene: Near the PHLPP1 gene/Trait: Straight hair
#' rs11213819/Gene: Near the C11orf53 gene/Trait: Less likely to
#' sneeze after eating dark chocolate
#'
#' NOTE! MyHeritage genotypes do not report some if the SNPs, however missing
#' genotypes can be imputed and accessed by DNALand imputation tool
#'
#' !!!! myAllele column reports whether risk allele was identified in my genome
#'
#' @import stringr
#'
#' @examples
#'
#' \dontrun{
#' # example myHeritage
#' library(myDNA)
#' library(dplyr)
#' library(stringr)
#' Genome="/data/akalin/Projects/AAkalin_myDNA/Data/MyHeritage/MyHeritage_raw_dna_dataInga/MyHeritage_raw_dna_data.csv"
#' myDNA <- importDNA(myGenotypes = Genome,type = "myHeritage" )
#' neanderthalMe(myDNA)
#' }
#' @author Inga Patarcic
#' @export
neanderthalMe <- function(myDNA) {
SCREEN <- myDNAScreenSNPS(myDNA = myDNA,
snpsData = cbind(c("rs7544462",
"rs1877547",
"rs4849721",
"rs12458349",
"rs11213819"),
c("C","A","T","G","T")))
if (nrow(SCREEN)==0) {
stop("SNP not present in the genotype data, try with imputed dataset")}
if (nrow(SCREEN)!=0) {return(SCREEN)}
}
###########################################
# --- screen for red hair ---
###########################################
#' Function to screen for red hairiness
#'
#'
#' @param myDNA (character) path to the genotype file
#'
#' @details
#' SOURCE 1: 23andMe report
#' NOTE! MyHeritage genotypes do not report some if the SNPs, however missing
#' genotypes can be imputed and accessed by DNALand imputation tool
#' INFO:
#' Several variants in a single gene, MC1R, can cause red hair by increasing
#' the amount of pheomelanin in your hair.
#' Hair color is determined by not just how much pigment you have,
#' but also what kind. Whether you have red hair depends on your levels of
#' red/yellow pigment (pheomelanin). But the lightness or darkness of your hair
#' depends on your levels of a brown/black pigment called eumelanin
#' REPORTED SNPS: rs1805007,rs1805008,i3002507
#'
#' SOURCE 2: https://www.snpedia.com/index.php/I3002507
#' i3002507 alias rs1805009 identified in SNPedia
#' proxy calculations needed
#'
#' !!!! myAllele column reports whether risk allele was identified in my genome
#'
#' @import stringr
#'
#' @examples
#'
#' \dontrun{
#' # example myHeritage
#' library(myDNA)
#' library(dplyr)
#' library(stringr)
#' Genome="/data/akalin/Projects/AAkalin_myDNA/Data/MyHeritage/MyHeritage_raw_dna_dataInga/MyHeritage_raw_dna_data.csv"
#' myDNA <- importDNA(myGenotypes = Genome,type = "myHeritage" )
#' redHair(myDNA)
#' }
#' @author Inga Patarcic
#' @export
redHair <- function(myDNA) {
SCREEN <- suppressWarnings(myDNAScreenSNPS(myDNA = myDNA,
snpsData = cbind(c("rs1805007",
"rs1805008",
"rs1805009"),
c("T","T","C"))))
if (nrow(SCREEN)==0) {
stop("SNP not present in the genotype data, try with imputed dataset")}
if (nrow(SCREEN)!=0) {return(SCREEN)}
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.