Description Usage Arguments Details Note See Also Examples

Utility functions for accessing data in `SnpSet`

objects.

1 2 3 4 |

`object` |
A SnpSet object. |

`transform` |
Logical. Whether to transform the integer representation of the confidence score (for memory efficiency) to a probability. See details. |

`value` |
A matrix. |

`calls`

returns the genotype calls. CRLMM stores genotype calls
as integers (1 - AA; 2 - AB; 3 - BB).

`confs`

returns the confidences associated with the genotype
calls. The current implementation of CRLMM stores the confidences as
integers to save memory on disk by using the transformation:

round(-1000*log2(1-p)),

where 'p' is the posterior probability of the call. `confs`

is
a convenience function that transforms the integer representation
back to a probability. Note that if the assayData elements of the
`SnpSet`

objects are `ff_matrix`

or `ffdf`

, the
`confs`

function will return a warning. For such objects, one
should first subset the `ff`

object and coerce to a matrix,
then apply the above conversion. The function
`snpCallProbability`

for the `callProbability`

slot of
`SnpSet`

objects. See the examples below.

`checkOrder`

checks whether the object is ordered by chromosome
and physical position, evaluating to TRUE or FALSE.

Note that the replacement method for `confs<-`

expects a matrix
of probabilities and will automatically convert the probabilities to
an integer representation. See details for the conversion.

The accessor `snpCallProbability`

is an accessor for the
'callProbability' element of the `assayData`

. The name can be
misleading, however, as the accessor will not return a probability if
the call probabilities are represented as integers.

The helper functions `p2i`

converts probabilities to
integers and `i2p`

converts integers to probabilities.

See `order`

and `checkOrder`

.

1 2 3 4 5 6 7 8 | ```
theCalls <- matrix(sample(1:3, 20, rep=TRUE), nc=2)
p <- matrix(runif(20), nc=2)
integerRepresentation <- matrix(as.integer(round(-1000*log(1-p))), 10, 2)
obj <- new("SnpSet2", call=theCalls, callProbability=integerRepresentation)
calls(obj)
confs(obj) ## coerces to probability scale
int <- Biobase::snpCallProbability(obj) ## not necessarily a probability
p3 <- i2p(int) ## to convert back to a probability
``` |

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