show_result_haystack | R Documentation |
Shows the results of the 'haystack' analysis in various ways, sorted by significance. Priority of params is genes > p.value.threshold > n.
show_result_haystack( res.haystack, n = NULL, p.value.threshold = NULL, gene = NULL ) ## S3 method for class 'haystack' show_result_haystack( res.haystack, n = NULL, p.value.threshold = NULL, gene = NULL )
res.haystack |
A 'haystack' result object. |
n |
If defined, the top "n" significant genes will be returned. Default: NA, which shows all results. |
p.value.threshold |
If defined, genes passing this p-value threshold will be returned. |
gene |
If defined, the results of this (these) gene(s) will be returned. |
The output is a data.frame with the following columns: * D_KL the calculated KL divergence. * log.p.vals log10 p.values calculated from randomization. * log.p.adj log10 p.values adjusted by Bonferroni correction.
A data.frame with 'haystack' results sorted by log.p.vals.
# using the toy example of the singleCellHaystack package # running haystack res <- haystack(dat.tsne, dat.expression) # below are variations for showing the results in a table # 1. list top 10 biased genes show_result_haystack(res.haystack = res, n =10) # 2. list genes with p value below a certain threshold show_result_haystack(res.haystack = res, p.value.threshold=1e-10) # 3. list a set of specified genes set <- c("gene_497","gene_386", "gene_275") show_result_haystack(res.haystack = res, gene = set)
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