Description Usage Arguments Value Author(s) See Also
These generic functions provide access to variables associated with GWAS data cleaning.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 | getScanAnnotation(object, ...)
getScanVariable(object, varname, ...)
getScanVariableNames(object, ...)
getScanID(object, ...)
getSex(object, ...)
getSnpAnnotation(object, ...)
getSnpVariable(object, varname, ...)
getSnpVariableNames(object, ...)
getSnpID(object, ...)
getChromosome(object, ...)
getPosition(object, ...)
getAlleleA(object, ...)
getAlleleB(object, ...)
getVariable(object, varname, ...)
getVariableNames(object, ...)
getGenotype(object, ...)
getGenotypeSelection(object, ...)
getQuality(object, ...)
getX(object, ...)
getY(object, ...)
getBAlleleFreq(object, ...)
getLogRRatio(object, ...)
getDimension(object, varname, ...)
getAttribute(object, attname, varname, ...)
getNodeDescription(object, varname, ...)
getAnnotation(object, ...)
getMetadata(object, ...)
getQuery(object, statement, ...)
hasScanAnnotation(object)
hasScanVariable(object, varname)
hasSex(object)
hasSnpAnnotation(object)
hasSnpVariable(object, varname)
hasVariable(object, varname)
hasQuality(object)
hasX(object)
hasY(object)
hasBAlleleFreq(object)
hasLogRRatio(object)
nsnp(object)
nscan(object)
autosomeCode(object)
XchromCode(object)
XYchromCode(object)
YchromCode(object)
MchromCode(object)
writeAnnotation(object, value, ...)
writeMetadata(object, value, ...)
|
object |
Object, possibly derived from or containing
|
varname |
Name of the variable (single character string, or a character vector for multiple variables). |
attname |
Name of an attribute. |
statement |
SQL statement to query
|
value |
data.frame with annotation or metadata to write to
|
... |
Additional arguments. |
get
methods return vectors or matrices of the requested
variables (with the exception of getQuery
, which returns a data
frame).
has
methods return TRUE if the requested variable
is present in object
.
nsnp
and nscan
return the number of SNPs and scans in
the object, repectively.
autosomeCode
, XchromCode
, XYchromCode
, YchromCode
, and
MchromCode
return the integer chromosome codes associated with
autosomal, X,
pseudoautosomal, Y, and mitochondrial SNPs.
Stephanie Gogarten
ScanAnnotationDataFrame-class
,
SnpAnnotationDataFrame-class
,
ScanAnnotationSQLite-class
,
SnpAnnotationSQLite-class
,
NcdfReader-class
,
NcdfGenotypeReader-class
,
NcdfIntensityReader-class
,
GdsReader-class
,
GdsGenotypeReader-class
,
GdsIntensityReader-class
,
GenotypeData-class
, IntensityData-class
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