mine_step3 {cageminer}R Documentation

Step 3: Select candidates based on gene significance

Description

Step 3: Select candidates based on gene significance

Usage

mine_step3(
  exp,
  metadata,
  candidates,
  sample_group,
  min_cor = 0.2,
  alpha = 0.05,
  continuous = FALSE
)

Arguments

exp

Expression data frame with genes in row names and samples in column names or a SummarizedExperiment object.

metadata

Sample metadata with samples in row names and sample information in the first column. Ignored if exp is a SummarizedExperiment object, as the colData will be extracted from the object.

candidates

Character vector of candidate genes to be inspected.

sample_group

Level of sample metadata to be used for filtering in gene-trait correlation.

min_cor

Minimum correlation value for BioNERO::gene_significance(). Default: 0.2

alpha

Numeric indicating significance level. Default: 0.05

continuous

Logical indicating whether metadata is continuous or not. Default: FALSE

Value

A data frame with mined candidate genes and their correlation to the condition of interest.

Examples

data(pepper_se)
data(snp_pos)
data(gene_ranges)
data(guides)
data(gcn)
data(mine2)
set.seed(1)
mine3 <- mine_step3(pepper_se, candidates = mine2$candidates,
                    sample_group = "PRR_stress")

[Package cageminer version 0.99.7 Index]