Description Usage Arguments Value Examples
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.
1 2 3 4 5 |
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 |
Returns the name of the file created.
1 2 3 4 5 6 7 8 9 10 11 12 | ## 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)
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