maskedStrandCheck: Plot masked variant strand check
In sarahcn/impplotr: Summarize Metrics from University of Michigan Imputation Server
Description
Usage
Arguments
Value
View source: R/plotting_functions.R
Description
Plot masked variant strand check
Usage
1
maskedStrandCheck(out_dir, start_chr, end_chr, mets_all)
Arguments
out_dir
Output directory
start_chr
Start chromosome (1:23)
end_chr
End chromosome (1:23)
mets_all
Dataframe of imputation metrics created by readMetrics
Value
Scatterplot of masked variant metrics that can help identify systematic strand alignment issues
Caveat the resulting plot can be messy. Read the log file to understand the count of variants in the problematic quadrant: those imputed with high confidence but low concordance.
sarahcn/impplotr documentation built on May 3, 2019, 9 p.m.
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Description Usage Arguments Value
View source: R/plotting_functions.R
Description
Plot masked variant strand check
Usage
1 | maskedStrandCheck(out_dir, start_chr, end_chr, mets_all)
|
Arguments
out_dir |
Output directory |
start_chr |
Start chromosome (1:23) |
end_chr |
End chromosome (1:23) |
mets_all |
Dataframe of imputation metrics created by |
Value
Scatterplot of masked variant metrics that can help identify systematic strand alignment issues Caveat the resulting plot can be messy. Read the log file to understand the count of variants in the problematic quadrant: those imputed with high confidence but low concordance.
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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