show_result_haystack: show_result_haystack

In alexisvdb/singleCellHaystack: A Universal Differential Expression Prediction Tool for Single-Cell and Spatial Genomics Data

show_result_haystack

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 = 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
)

Arguments

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.

Details

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.

Value

A data.frame with 'haystack' results sorted by log.p.vals.

Examples

# 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)

alexisvdb/singleCellHaystack documentation built on Jan. 17, 2024, 10:45 a.m.