| KSR.list | R Documentation |
KSR.list returns a list of kinase substrate relationships
KSR.list(df, kinasefamilies = NULL, exclusive = FALSE)
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) |
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.
named list of substrate identifiers, with the corresponding kinase identifiers as the list names
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)