singleCellHaystack (version 0.3.4)

show_result_haystack: Shows the results of the 'haystack' analysis in various ways, sorted by significance. Priority of params is genes > p.value.threshold > n.

Description

Shows the results of the 'haystack' analysis in various ways, sorted by significance. Priority of params is genes > p.value.threshold > n.

Usage

show_result_haystack(res.haystack, n = NA, p.value.threshold = NA, gene = NA)

Value

A table with a sorted subset of the 'haystack' result according to input parameters.

Arguments

res.haystack

A 'haystack' result variable

n

If defined, the top "n" sigificant 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.

Examples

# using the toy example of the singleCellHaystack package
# define a logical matrix with detection of each gene (rows) in each cell (columns)
dat.detection <- dat.expression > 1

# running haystack in default mode
res <- haystack(dat.tsne, detection=dat.detection, method = "2D")

# 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)