ksrlive (version 1.0)

KSR.list: Create a kinase substrate relationship list from a data frame

Description

KSR.list returns a list of kinase substrate relationships

Usage

KSR.list(df, kinasefamilies = NULL, exclusive = FALSE)

Arguments

df

data frame of kinase substrate relationships with substrate identifier in the first column and kinase identifier in the second column.

kinasefamilies

named list of kinase identifiers that have to be combined, one list per kinase family, list will be named after first family member

exclusive

logical, if TRUE only substrates exclusive to the kinase will be included in the list (substrates with multiple kinases will be excluded)

Value

named list of substrate identifiers, with the corresponding kinase identifiers as the list names

Details

The function KSR.list creates a list of kinase substrate relationships from a data frame and can combine kinase families into one list. Substrates occuring in multiple lists can be excluded.

Examples

data(phosphonetworkdf)
data(datakin)

# first column has to be substrate id, second kinase id
kin_data <- KSR.list(phosphonetwork_df[, c("SUB_IDENT", "KIN_ACC_ID")]) 
# Akt1 and Akt2 belong to the same kinase family, combine their substrates 
# into one list and name the list after the first family member
fam <- list(akt = c("P31749", "P31751"))
kin_data_fam <- KSR.list(phosphonetwork_df[, c("SUB_IDENT", "KIN_ACC_ID")], 
kinasefamilies = fam)

# only include phosphosites appearing once
kin_data_fam_exc <- KSR.list(phosphonetwork_df[, c("SUB_IDENT", "KIN_ACC_ID")], 
                             kinasefamilies = fam,
                             exclusive = TRUE)