construct_pwm: Construct position weight matrix

In ecnuzdd/PhosMap: A Comprehensive R Package For Analyzing Quantitative Phosphoproteomics Data

Construct position weight matrix

Description

Construct position weight matrix

Usage

construct_pwm(sequences, width, frequency_flag = TRUE)

Arguments

sequences	A vector for aligned sequences with fixed length.
width	A numeric for specific k-mer.
frequency_flag	A boolean for showing real frequency or frequency probability, the default is TRUE for showing real frequency.

Value

A position weight matrix.

Author(s)

Dongdong Zhan and Mengsha Tong

References

Wagih O, Sugiyama N, Ishihama Y, et al. Uncovering phosphorylation-based specificities through functional interaction networks[J]. Molecular & Cellular Proteomics, 2016, 15(1): 236-245.

Examples

## Not run: 
ftp_url <- "ftp://111.198.139.72:4000/pub/PhosMap_datasets/function_demo_data/construct_pwm.RData"
load_data <- load_data_with_ftp(ftp_url, 'RData')
writeBin(load_data, "construct_pwm.RData")
load("construct_pwm.RData")

foreground_pwm <- construct_pwm(
 foreground_sequence,
 width,
 frequency_flag = TRUE
)
head(foreground_pwm)

## End(Not run)

ecnuzdd/PhosMap documentation built on Dec. 7, 2022, 4:09 a.m.