fragment.coverage: Plot fragment coverage

Description Usage Arguments Value Examples

View source: R/frag_cov.R

Description

These functions generate a map of fragmentation sites within a given protein sequence.

fragment.coverage plots fragment coverage based on BUPID results.

The fragment coverage image can also be called using a generic non-bupid format. Data in the generic function takes the form data.frame(term=c("C","N"),num=c(1,50)), where term is the protein terminus the fragment is generated from, and num is the fragment number or length in amino acids.

Usage

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fragment.coverage(data, file = "cov.svg", columns = 25L, scale = 2,
  color = c("#00f", "#f00", "#000"), marksite = NULL)

fragment.coverage.generic(data, sequence, file = "cov.svg", columns = 25L,
  scale = 2, color = c("#00f", "#f00", "#000"), marksite = NULL)

Arguments

data

a bupid object; output from read.bupid

file

the output file name

columns

the number of columns (residues per line) to use for the sequence

scale

magnification factor for the image

color

a length 3 character vector indicating the color C-term, N-term, and other fragments should be colored respectively. Also valid are NULL to make them all black or a length 1 character vector to make them all that color.

marksite

site numbers to place a marker at

sequence

protein sequence used in assignments

Value

Returns the name of the file created.

Examples

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## Not run: 
#bupid version
server <- "http://bupid.bumc.bu.edu/cgi-bin/get_results.cgi"
infile <- "key=WBNqTswT5DPg3aDO&ID=320&date=20150309"
data <- read.bupid(url=paste(server,infile,sep="?"))
fragment.coverage(data,file="136_coverage.svg",columns=50)

#generic version
data <- data.frame(term=c("N","N","C","C"),num=c(1,2,1,2))
fragment.coverage.generic(data,"ACDEF",file="generic_coverage.svg",scale=3,color=F)

## End(Not run)

heckendorfc/BTDR documentation built on April 28, 2018, 10:12 a.m.