Description Usage Arguments Details Value Author(s)
readGeno
reads genotype data stored in ped/map files, adjusts format for GenABEL package and processes it for further analysis.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | 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"
)
|
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 |
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 |
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 |
GTarrayDescription.lines2skip.end |
Numeric with number of rows to read when loading |
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. |
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.
GenABEL gwaa object
Frank Ruehle
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