Description Usage Arguments Value See Also Examples
QQ plots
1 2 |
results |
Results datarame from "get_results()" |
by |
Visualize results by "trait" OR by "set" |
plot_all |
plot_all = TRUE plots all the variables in the results dataframe and saves a pdf file in the working directory. Setting plot_all to FALSE plots a single variable(trait or set). The argument "var" must be declared. |
var |
Variable name to plot |
save_plot |
save_plot = TRUE saves the plots in the working directory. save_plot = FALSE the plot is visualized at the console. save_plot = FALSE can be used only when plot_all is set to FALSE. The plot displayed at the console is interactive, clicking on a point displays the points name. |
plot_name |
Argument used to save the file name for the plots. Default value = Results_genomicper_[set/trait] |
bf |
Displays the bonferroni correction |
save_qq |
TRUE returns the qq plot values |
qq |
Data frame with qq plot values |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 | data(demo,SNPsAnnotation)
all_data <- read_pvals(data_name=demo,snps_ann=SNPsAnnotation)
genome_results <-genome_order(all_data=all_data)
# Results from genome_order
ordered_alldata <- genome_results$ordered_alldata
gs_locs <- genome_results$gs_locs
# Create new environment to save the data:
gper.env <- new.env()
# Load Pathways
data(RHSA164843,RHSA446343,RHSA8876384,RHSA8964572,RHSA109582,RHSA1474244,envir=gper.env)
paths_res <- read2_paths(ordered_alldata=ordered_alldata,gs_locs=gs_locs,
sets_from="workspace",sets_prefix="RHSA",level="snp",envir=gper.env)
pers_ids <- paths_res$per_ors
pathways<- paths_res$pathways
snps_permutation(ordered_alldata=ordered_alldata,pers_ids=pers_ids,
ntraits=c(7,9),nper=10,saveto="workspace",threshold=0.05,
gs_locs=gs_locs,envir = gper.env)
results <- get_results(res_pattern="Permus",level="snp",
from="workspace",threshold=0.05,envir = gper.env)
#saves plots to working directory
## Not run:
qq <- plot_results(results=results,by="set",plot_all=TRUE)
qq <- plot_results(results=results,by="trait",plot_all=FALSE,var="trait1")
qq <- plot_results(results=results,by="set",
plot_all=FALSE,var="R-HSA-8964572",
save_plot=FALSE) ## IMPORTANT: to EXIT interactive plot
## right click on the plot to stop
## End(Not run)
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