predictKinasePhosphosites: Compute posterior probability of wild type phosphosites for...

In omarwagih/rmimp: Predicting the impact of mutations on kinase-substrate phosphorylation

Description

Compute posterior probability of wild type phosphosites for kinases

Usage

predictKinasePhosphosites(psites, seqs, model.data = "hconf",
  posterior_thresh = 0.8, intermediate = F, kinases)

Arguments

psites	phosphorylation data, see ?mimp for details
seqs	sequence data, see ?mimp for details
model.data	MIMP model used, see ?mimp for details
posterior_thresh	posterior probability threshold that the score belongs to the foreground distribution of the kinase, probabilities below this value are discarded (default 0.8)
intermediate	if TRUE intermediate MSS scores and likelihoods are reported (default FALSE)
kinases	vector of kinases used for the scoring (e.g. c("AURKB", "CDK2")), if this isn't provided all kinases will be used .

Value

The data is returned in a data.frame with the following columns:

gene	Gene with the rewiring event
pos	Position of the phosphosite
wt	Sequence of the wildtype phosphosite
score_wt	(intermediate value) matrix similarity score of sequence
l.wt.fg	(intermediate value) likelihood of score given foreground distribution
l.wt.bg	(intermediate value) likelihood of score given background distribution
post.wt.fg	posterior probability of score in foreground distribution
post.wt.bg	posterior probability of score in background distribution
pwm	Name of the predicted kinase
pwm_fam	Family/subfamily of the predicted kinase. If a kinase subfamily is available the family and subfamily will be seprated by an underscore e.g. "DMPK_ROCK". If no subfamily is available, only the family is shown e.g. "GSK"

Examples

# Get the path to example phosphorylation data 
psite.file = system.file("extdata", "sample_phosphosites.tab", package = "rmimp")

# Get the path to example FASTA sequence data 
seq.file = system.file("extdata", "sample_seqs.fa", package = "rmimp")

# Run for all kinases
results_all = predictKinasePhosphosites(psite.file, seq.file)

# Run for select kinases
results_select = predictKinasePhosphosites(psite.file, seq.file, kinases=c("AURKB", "CDK2"))

omarwagih/rmimp documentation built on May 18, 2020, 3:11 p.m.