buildPWM: Generate Position Weight Matrices (PWMs)
In awaardenberg/KinSwingR: KinSwingR: network-based kinase activity prediction

Description Usage Arguments Value Examples

Generate Position Weight Matrices (PWMs) for a table containing centered substrate peptide sequences for a list of kinases. The output of this function is to be used for scoring PWM matches to peptides via scoreSequences()

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buildPWM(kinase_table = NULL, wild_card = "_", substrate_length = 15,
  substrates_n = 10, pseudo = 0.01, remove_center = FALSE,
  verbose = FALSE)

`kinase_table`	A data.frame of substrate sequences and kinase names. Format of data must be as follows: column 1 - kinase/kinase family name/GeneID, column 2 - centered peptide seqeuence.
`wild_card`	Letter to describe sequences that are outside of the protein after centering on the phosphosite (e.g ___MERSTRELCLNF). Default: "_".
`substrate_length`	Full length of substrate sequence (default is 15). Will be trimmed automatically or report error if sequences in kinase_table are not long enough.
`substrates_n`	Number of sequences used to build a PWM model. Low sequence counts will produce poor representative PWM models. Default: "10"
`pseudo`	Small number to add to values for PWM log transformation to prevent log transformation of zero. Default = 0.01
`remove_center`	Remove all peptide seqeuences with the central amino acid matching a character (e.g. "y"). Default = FALSE
`verbose`	Print progress to screen. Default=FALSE

Output is a list containing two tables, "pwm" and "kinase". To access PWMs: pwms$pwm and Table of Kinase and sequence counts: pwms$kinase

## Build PWM models from phosphositeplus data with default of minimum
## of 10 substrate sequences for building a PWM model.

data(phosphositeplus_human)

##randomly sample 1000 substrates for demonstration.
set.seed(1)
sample_pwm <- phosphositeplus_human[sample(nrow(phosphositeplus_human), 
1000),]
pwms <- buildPWM(sample_pwm)

## Data frame of models built and number of sequences used to build each
## PWM model:
head(pwms$kinase)