comparePath: To conduct defferential activation test in select.ident...

In yingyonghui/CommPath:

To conduct defferential activation test in select.ident between two CommPath objects

Description

To conduct defferential activation test in select.ident between two CommPath objects

Usage

comparePath(
  object.1,
  object.2,
  select.ident,
  method = "t.test",
  p.adjust = "BH",
  min.size = 10,
  only.posi = FALSE,
  only.sig = TRUE,
  ...
)

Arguments

object.1	CommPath object 1
object.2	CommPath object 2 for comparison
select.ident	Identity class of interest
method	Method used for differential expression test, either 't.test' or 'wilcox.test'
p.adjust	Method used for p value correction for multiple differential expression test; see p.adjust function for more information
min.size	Minimum size of overlaping genes between candidate pathways and the expression matrix
only.posi	only logFC > 0
only.sig	only p_val_adj < 0.05
...	Extra parameters passed to GSVA::gsvaParam

Value

Data frame of differentially activated pathways between the same clusters in two CommPath object

yingyonghui/CommPath documentation built on June 15, 2025, 6:29 a.m.