mtAnno: mtAnno function

In mtDNA-BU/mtdnaANNO: Annotation of mtDNA sequence variations

mtAnno function

Description

Annotate Given Alternative Alleles of mtDNA Loci.

Usage

mtAnno(
  anno,
  annot.select = c("Pos", "ref", "Gene", "TypeMutation", "MissensMutation",
    "CodonPosition", "ProteinDomain", "dbSNP_150_id", "PolyPhen2", "PolyPhen2_score",
    "SIFT", "SIFT_score", "CADD", "CADD_score", "CADD_phred_score"),
  path = "./",
  study = "Study"
)

Arguments

anno	a data frame provided by the user. It has two columns: mtDNA loci positions ("pos") and alternative alleles ("alleles") to be annotated.
annot.select	A character vector of variation position, alternative allele, corresponding gene and types of annotation scores to output based on user's choice. The available choices are "Pos", "ref", "Gene", "TypeMutation", "MissensMutation", "CodonPosition", "ProteinDomain", "mFOLD_dG", "mFOLD_Initial", "mFOLD_rCRS.DG", "mFOLD_rCRS.Initial", "mFOLD_AnticodonAminoAcidChange", "mFOLD_Location", "PolyPhen2", "PolyPhen2_score", "SIFT", "SIFT_score", "PROVEAN", "PROVEAN_score", "MutationAssessor", "MutationAssessor_score", "CADD", "CADD_score", "CADD_phred_score", "PANTHER", "PANTHER_score", "PhD_SNP", "PhD_SNP_score", "SNAP", "SNAP_score", "MutationTaster", "MutationTaster_score", "dbSNP_150_id", "APOGEE_boost_consensus", "APOGEE_boost_mean_prob", "APOGEE_boost_mean"
path	the path to the directory of the output of annotation file. If not provided, the annotation file will output to the current working directory.
study	A string of study names. Default is "Study".

Value

A .csv file containing annotated alternative alleles with corresponding mtDNA loci positions.

Examples

## Not run: 
## Read input data
allele_file <- "allele.csv"
freq_file   <- "freq.csv"

allele <- as.matrix( read.csv(file = allele_file, sep = ",", header=FALSE) )
freq   <- as.matrix( read.csv(file = freq_file, sep = ",", header=FALSE) )

aaf =  mtAAF ( allele, freq)

## Annotate Given Alternative Alleles of mtDNA Loci
mtAnno(aaf)

##
mtAnno(aaf, annot.select=c("ref","Gene") )

## End(Not run)

mtDNA-BU/mtdnaANNO documentation built on Aug. 11, 2022, 10:57 a.m.