run_hmm: A function that assigns the position in each gamete to the...
In mccoy-lab/rhapsodi: R haploid sperm/oocyte data imputation
run_hmm R Documentation
A function that assigns the position in each gamete to the correct donor haplotype
Description
This function walks along each gamete and replaces the original observation with the inferred state.
If the number of original observations is 0 or 1, the viterbi algorithm is not called, as there is no "path" to evaluate.
If only one observation, we assign the one observation as the inferred state
If no observations, we assign an inferred state of NA, such that the inferred state (NA) simply matches the original observations (which were also NA in this situation)
This replaces any incorrect haplotype assignments (e.g., due to sequencing error).
Usage
run_hmm(dt, column_index, hmm)
Arguments
dt
Matrix of gametes with 0 and 1
column_index
apply function cycles through gamete_dt to act on each column (i.e., each gamete)
hmm
the HMM that viterbi will be applied on
Value
original_obs Replaced observed haplotype with that assigned by the model
mccoy-lab/rhapsodi documentation built on July 27, 2022, 3:56 a.m.
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| run_hmm | R Documentation |
A function that assigns the position in each gamete to the correct donor haplotype
Description
This function walks along each gamete and replaces the original observation with the inferred state. If the number of original observations is 0 or 1, the viterbi algorithm is not called, as there is no "path" to evaluate. If only one observation, we assign the one observation as the inferred state If no observations, we assign an inferred state of NA, such that the inferred state (NA) simply matches the original observations (which were also NA in this situation) This replaces any incorrect haplotype assignments (e.g., due to sequencing error).
Usage
run_hmm(dt, column_index, hmm)
Arguments
dt |
Matrix of gametes with 0 and 1 |
column_index |
|
hmm |
the HMM that viterbi will be applied on |
Value
original_obs Replaced observed haplotype with that assigned by the model
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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