dupGet {rCNV} | R Documentation |
Detect deviants from SNPs; classify SNPs
Description
Detect deviant SNPs using excess of heterozygotes (alleles that do not follow HWE) and allelic-ratio deviations (alleles with ratios that do not follow a normal Z-score or chi-square distribution). See details.
Usage
dupGet(
data,
test = c("z.het", "z.05", "z.all", "chi.het", "chi.05", "chi.all"),
intersection = FALSE,
method = c("fisher", "chi.sq"),
plot = TRUE,
verbose = TRUE,
...
)
Arguments
data |
data frame of the output of |
test |
character. type of test to be used for significance. See details |
intersection |
logical, whether to use the intersection of the methods
specified in |
method |
character. method for testing excess of heterozygotes.
Fisher exact test ( |
plot |
logical. whether to plot the detected singlets and duplicates on allele ratio vs. proportion of heterozygotes plot. |
verbose |
logical. show progress |
... |
additional parameters passed on to |
Details
SNP deviants are detected with both excess of heterozygosity according to HWE and deviant SNPs where depth values fall outside of the normal distribution are detected using the following methods:
Z-score test
Z_{x} = \sum_{i=1}^{n} Z_{i}
;Z_{i} = \frac{\left ( (N_{i}\times p)- N_{Ai} \right )}{\sqrt{N_{i}\times p(1-p)}}
chi-square test
X_{x}^{2} = \sum_{i-1}^{n} X_{i}^{2}
;X_{i}^{2} = (\frac{(N_{i}\times p - N_{Ai})^2}{N_{i}\times p} + \frac{(N_{i}\times (1 - p)- (N_{i} - N_{Ai}))^2}{N_{i}\times (1-p)})
See references for more details on the methods
Users can pick among Z-score for heterozygotes (z.het, chi.het
),
all allele combinations (z.all, chi.all
) and the assumption of no
probe bias p=0.5 (z.05, chi.05
)
Value
Returns a data frame of snps/alleles with their duplication status
Author(s)
Piyal Karunarathne
Examples
## Not run: data(alleleINF)
DD<-dupGet(alleleINF)
## End(Not run)