readGeno: Read Genotype Data Using GenABEL.

In frankRuehle/systemsbio: Streamlined Analysis and Integration of Systems Biology Data

Description

readGeno reads genotype data stored in ped/map files, adjusts format for GenABEL package and processes it for further analysis.

Usage

readGeno(
  genoFilename,
  mapFilename,
  covarFilename,
  existingRawFile = NULL,
  covarsampleID = "IID",
  sexvar = "Gender",
  projectfolder = "GT",
  projectname = NULL,
  organism = "human",
  Gonosomes2char = T,
  removeNullPositions = T,
  updateSNPpos = NULL,
  snpmart = useMart("ENSEMBL_MART_SNP", host = "feb2014.archive.ensembl.org", dataset =
    "hsapiens_snp"),
  GTarrayDescriptionFile = NULL,
  GTarrayDescription.lines2skip.start = "\\[Assay\\]",
  GTarrayDescription.lines2skip.end = "\\[Controls\\]",
  GTarrayDescription.colname.identifier = "Name",
  GTarrayDescription.colname.coding = "SNP",
  GTarrayDescription.colname.strand = "RefStrand",
  GTarrayDescription.colname.chromosome = "Chr",
  GTarrayDescription.colname.position = "MapInfo"
)

Arguments

genoFilename	Character with path to ped file.
mapFilename	Character with path to map file.
covarFilename	Character with path to covariates file (gender information is needed).
existingRawFile	Character with path to an optionally already existing GenABEL Raw which will preferably loaded and supersedes any other files. Omitted if NULL.
covarsampleID	Character with column name of sample IDs in covar file.
sexvar	Character with column name indicating gender in covar file.
projectfolder	Character containing path to output folder (will be generated if not existing).
projectname	Character used as suffix for output files.
organism	Character with name of organism (e.g. "human").
Gonosomes2char	Boolean. If TRUE, chromosome names 23, 24, 25, 26 will be converted to X, Y, XY, MT (for human only).
removeNullPositions	Boolean. If TRUE, SNPs with Chr=0 or Pos=0 or NA will be removed from generated gwaa object
updateSNPpos	Character with value "biomaRt" or "descriptionfile". For "biomaRt", chromosome and SNP positions in map-file will be updated by biomaRt. If "descriptionfile", they will be updated by the supplied GTarrayDescriptionFile. If NULL chromosome and SNP positions are not updated.
snpmart	biomaRt object to be used for updating SNP positions (or NULL).
GTarrayDescriptionFile	Optional character with path to Illumina array description file. If given, strand and allele coding data will be added to map file.
GTarrayDescription.lines2skip.start	Numeric with number of rows to skip when loading annotationFile or regular expression for character string to identify corresponding row number to be skipped, e.g. [Assay] in Illumina annotation files.
GTarrayDescription.lines2skip.end	Numeric with number of rows to read when loading annotationFile or regular expression for character string to identify corresponding row number to be read, e.g. [Controls] in Illumina annotation files as start of annotation of control probes. All rows from that number on (incl. GTarrayDescription.lines2skip.end) are skipped.
GTarrayDescription.colname.identifier	Character with colnames for SNP identifier in Array description file.
GTarrayDescription.colname.coding	Character with colnames for allele coding information.
GTarrayDescription.colname.strand	Character with colnames for strand information.
GTarrayDescription.colname.chromosome	Character with colnames for chromosome name.
GTarrayDescription.colname.position	Character with colnames for pb position.

Details

If a GenABEL raw data file given in existingRawFile already exists, this file is directly loaded into a gwaa object. Otherwise this file has to be created first from the supplied ped and map file. For this, the map file in mapFilename is loaded, the linkage column (column 3) removed if present and a headerline is added. If an Array description file is supplied in GTarrayDescriptionFile, an extended map file is generated for GenABEL including strand and allele coding information. Otherwise strand information is set to unknown. If indicated in updateSNPpos SNP chromosomal postions can be updated according either to biomaRt (if a biomaRt object is given in snpmart) or to GTarrayDescriptionFile. Mind that GenABEL does not allow strings of characters as alleles in the corresponding ped-file (as for Indels), but just 1-character-alleles or "-".

After loading the GenABEL raw file, phenotype information is added from the supplied covariates file covarFilename. I.e. no phenotype or gender data is considered from initial ped-file. No white space allowed in phenotype entries. No missing data allowed in gender column given in sexvar. All samples from geno file must have entries in pheno-file. For 1/2-coded binary phenotypes additional 0/1-coded phenotypes are generated (stored with suffix "01"). If gender is 1/2 (1=male, 2=female) coded in sexvar, a new variable sex is generated 0/1 coded (1=male, 0=female) as required by GenABEL. Optionally, numeric gonosome names can be converted to character names (e.g. "X", "Y"). If removeNullPositions is set TRUE, variants without valid coordinates are removed from the generated gwaa dataset.

Value

GenABEL gwaa object

Author(s)

Frank Ruehle

frankRuehle/systemsbio documentation built on Sept. 14, 2020, 1:18 a.m.