phoenics (version 0.5)

pathwayRes: Class pathwayRes

Description

S3 class for pathway differential analysis results

Usage

# S3 method for pathwayRes
summary(object, ...)
# S3 method for pathwayRes
print(x, ...)
# S3 method for pathwayRes
plot(
  x,
  ...,
  pathway_id = NULL,
  plot = c("eig", "var", "ind", "group"),
  habillage = "none"
)
# S3 method for pathwayRes
head(x, ...)
extract(object, pathway_id)
adjust_pval(object, method = p.adjust.methods, n = length(object))

Value

The function extract returns an object of class pathwayRes which is a list of pathway results, containing only the pathways in pathway_id.

The function adjust_pval returns a data.frame with pathways in rows and the following information in columns:

pathway_name

name of the pathway

pathway_code

pathway code (identifier)

Fixed_effect

tested effect

pval

raw p-value of the pathway

adjusted_pval

adjusted p-value of the pathway

Arguments

object, x

object of class pathwayRes

...

not used

pathway_id

a character string or vector of pathway codes or names

plot

a character string indicating the type of plot to return. Default to "eig" (the screegraph of the PCA or MFA is displayed)

habillage

a character string indicating the column of the design used to color the individuals. Only used when plot = "ind". Default to "none" (no color)

method

a character string indicating the correction method to be used for multiple testing correction (authorized values are those of p.adjust.methods)

n

number of comparisons for multiple testing correction

Details

Methods for the class pathwayRes

Examples

data("MTBLS422")
quantif <- from_ASICS_to_PHOENICS(quantif)
out_test <- test_pathway(quantif, design, pathways, 
                         fixed = c("Age", "Treatment"), random = "Mouse", 
                         npc = 2, model = "blmer")
summary(out_test)
out_test2 <- test_pathway(quantif, design, pathways, 
                         fixed = c("Age", "Treatment"), random = "Mouse", 
                         npc = 2, model = "blmer", analysis = "MFA")
summary(out_test2)
print(out_test)
print(out_test2)
plot(out_test)
plot(out_test, pathway_id = "mmu00052", plot = "var")
plot(out_test, pathway_id = "mmu00052", plot = "ind", habillage = "Age")
plot(out_test2, pathway_id = "mmu00562", plot = "eig")
plot(out_test2, pathway_id = "mmu00562", plot = "var")
plot(out_test2, pathway_id = "mmu00562", plot = "ind")
plot(out_test2, pathway_id = "mmu00562", plot = "group")
extract(out_test, "mmu00562")
adj_pval <- adjust_pval(out_test)