🔖 release v0.9.7 #28
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🔖 release v0.9.7 #28
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a new output variable has been added to keep track of the average percentage of samples in which SNPs are "in runs" the new output variable is named avg_pct and is a column added at the end of the output data.frame
snpInsideRuns(Cpp) is now internal
check runs where SNP are major or equal the threshold specified
rewrite code to calculate percentages correctly
correctly skip empty subset
no more copy values from dataframe
…Runs Set guides(fill="none") since ggplot2 deprecated guides(fill=FALSE)
👽 set guides(fill="none") in plot_InbreedingChr and plot_DistributionRuns
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #28 +/- ##
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+ Coverage 51.11% 59.01% +7.89%
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Files 6 6
Lines 1254 1359 +105
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+ Hits 641 802 +161
+ Misses 613 557 -56 ☔ View full report in Codecov by Sentry. |
⚡ refactor tableRuns to better manage memory
- added a comment on the need for chromosomes to be numerically coded - in the vignette, the description of the `summary_ROH_mean_chr` dataset from `summaryRuns()` has been corrected - the documentation of the function `summaryRuns` has been expanded
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Ready to merge for me |
bunop
requested changes
May 25, 2023
| @@ -243,7 +243,16 @@ Froh_inbreedingClass <- function(runs, mapFile, Class=2){ | |||
| #' | |||
| #' @return A list of dataframes containing the most relevant descriptives | |||
| #' statistics on detected runs. The list conveniently contains 9 dataframes that can | |||
| #' be used for further processing and visualization, or can be written out to text files | |||
| #' be used for further processing and visualization, or can be written out to text files: | |||
| #' 1) summary_ROH_count_chr: n. of runs per chromosome and breed/group; | |||
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This list will be rendered as a plain text. Consider using list with roxygen, for example:
#' \enumerate{
#' \item{summary_ROH_count_chr: }{n. of runs per chromosome and breed/group}
#' \item{summary_ROH_percentage_chr: }{percent distribution of runs per chromosome in each breed/group (sum to 1)}
#' \item{summary_ROH_count: }{n. of runs per size-class (Mb) in each breed/group}
#' <add all the other items>
#' }| #' 6) summary_ROH_mean_class: average size of runs (Mb) per size-class (Mb) in each breed/group | ||
| #' 7) result_Froh_genome_wide: genome-wide inbreeding ($F_{ROH}$) for each individual in the dataset | ||
| #' 8) result_Froh_chromosome_wide inbreeding ($F_{ROH}$) for each individual (and chromosome) in the dataset | ||
| #' 9) result_Froh_class: genome-wide inbreeding ($F_{ROH}$) for each individual in the dataset per size-class (Mb) of runs |
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There could be a 10th item when providing snpInRuns=TRUE as parameter
| #' | ||
| #' @param genotypeFile genotype (.ped) file path | ||
| #' @param mapFile map file (.map) file path | ||
| #' @param mapFile map file (.map) file path (chromosomes should be numeric) |
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will be better to check chromosomes in readMapFile directly and throw an error here?
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Improving the output of the function
tableRunsDescription
On the
develbranch, the code of the functiontableRunshas been modified to add a column namedavg_pctto the output dataframeRelated Issue
close #43
close #39
close #31
close #36
close #17
Motivation and Context
It adds a piece of relevant information to the output of the function
tableRuns(ROH/HRR islands)How Has This Been Tested?
Types of changes
Checklist: