Nothing
## ----echo=TRUE----------------------------------------------------------------
library(KinSwingR)
data(example_phosphoproteome)
data(phosphositeplus_human)
# View the datasets:
head(example_phosphoproteome)
head(phosphositeplus_human)
## sample 100 data points for demonstration
sample_data <- head(example_phosphoproteome, 1000)
# Random sample for demosntration purposes
set.seed(1234)
sample_pwm <- phosphositeplus_human[sample(nrow(phosphositeplus_human), 1000),]
# for visualising a motif, sample only CAMK2A
CAMK2A_example <- phosphositeplus_human[phosphositeplus_human[,1]== "CAMK2A",]
## ----echo=TRUE----------------------------------------------------------------
annotated_data <- cleanAnnotation(input_data = sample_data,
annotation_delimiter = "|",
multi_protein_delimiter = ":",
multi_site_delimiter = ";",
seq_number = 4,
replace = TRUE,
replace_search = "X",
replace_with = "_")
head(annotated_data)
## ----echo=TRUE----------------------------------------------------------------
pwms <- buildPWM(sample_pwm)
## ----echo=TRUE----------------------------------------------------------------
head(pwms$kinase)
## ----echo=TRUE----------------------------------------------------------------
CAMK2A_pwm <- buildPWM(CAMK2A_example)
CAMK2A <- viewPWM(CAMK2A_pwm,
which_pwm="CAMK2A",
view_pwm = TRUE,
color_scheme = "shapely")
## ----echo=TRUE----------------------------------------------------------------
# As an example of control over multi-core processing
# load BiocParallel library
library(BiocParallel)
# finally set/register the number of cores to use
register(SnowParam(workers = 4))
# set seed for reproducible results
set.seed(1234)
scores <- scoreSequences(input_data = annotated_data,
pwm_in = pwms,
n = 100)
## ----echo=TRUE----------------------------------------------------------------
# after loading BiocParallel library, set/register the number of cores to use
register(SnowParam(workers = 4))
# set seed for reproducible results
set.seed(1234)
swing_out <- swing(input_data = annotated_data,
pwm_in = pwms,
pwm_scores = scores,
permutations = 10)
# This will produce two tables, one is a network for use with e.g. Cytoscape and the other is the scores. To access the scores:
head(swing_out$scores)
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