mine_step3 {cageminer} | R Documentation |
Step 3: Select candidates based on gene significance
mine_step3( exp, metadata, candidates, sample_group, min_cor = 0.2, alpha = 0.05, continuous = FALSE )
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 |
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
|
alpha |
Numeric indicating significance level. Default: 0.05 |
continuous |
Logical indicating whether metadata is continuous or not. Default: FALSE |
A data frame with mined candidate genes and their correlation to the condition of interest.
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")