Description Usage Arguments Details Value Author(s) Examples
extractBackground() extracts a list of background sequences (of a particular width centered around a specific character) from an input file for subsequent use with tools such as motif-x.
1 | extractBackground(sequences, central, width)
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sequences |
list of sequences from which background will be extracted. |
central |
a character denoting the central residue for the background you want to extract (eg. S for Serine). |
width |
an integer denoting the width of the motif you want to extract. |
output will be limited to background sequences that are at least the size of the specified width. Background sequences that are shorter than this width (due to being near termini of proteins) will be removed.
a list of strings
Jacob M. Wozniak (jakewozniak@gmail.com)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | # Locate example files
examples.path = system.file("extdata", package = "PTMphinder")
parsed_ref.path = paste(examples.path, "/Human_Uniprot_Parsed_Example.txt", sep="")
# Read in parsed Uniprot database example (or one you created with parseDB above)
parsed_ref <- read.table(parsed_ref.path, header=FALSE, row.names=NULL, sep="\t")
# Set parameters for extractBackground (s - sequence list; c - central character; w - width of motifs)
s <- unlist(parsed_ref[,2])
c <- "S"
w <- 15
# Extract proteome-specific background motifs (may take a while depending on database size)
extractBack_Example <- extractBackground(s, c, w)
# Create file name for background motif list
fileName2 <- paste(examples.path, "/Background_", c, "_" ,w, "_", Sys.Date(), ".txt", sep="")
# Write background motif list to new file (will be found in the PTMphinder/extdata/ directory within R.framework)
write.table(extractBack_Example, fileName2, row.names=FALSE, col.names=FALSE, quote=FALSE)
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