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+

+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

+##                                                                           ##

+##  Project   :   seqTools                                                   ##

+##  Created   :   26.August.2013                                             ##

+##  Author    :   W. Kaisers                                                 ##

+##  File      :   allStatics.r                                               ##

+##  Content   :   All static variables and (not directly object related )    ##

+##                function declarations                                      ##

+##                                                                           ##

+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

+

+

+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

+## Global variables:

+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

+

+strandlevels <- c("+", "-", "*")

+iupac_chars <- c('a', 'c', 'g', 't', 'u', 'r', 'y', 's', 'w', 'k', 'm', 'b',

+                'd', 'h', 'v', 'n', '.', '-', '=')

+

+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

+## Although static array sizes would allow larger k (e.g. 15: 8 GB RAM), 

+## exponential increase in run-time restricts usability to k values in 1:12

+## 4^12 = 16.777.216 possible combinations.

+## 'Hard' coded (in stat_defs.h: 15)

+max_k <- 12

+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

+

+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

+## End global variables

+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

+

+

+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

+## Some useful functions for work with phred's

+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

+

+char2ascii <- function(c) { strtoi(charToRaw(c), base=16L) }

+

+ascii2char <- function(x, multiple=FALSE)

+                                { rawToChar(as.raw(x), multiple=multiple) }

+

+phredTable <- function(phred=0:93)

+{

+    if(!is.numeric(phred))

+        stop("phred must be numeric.")

+    

+    phred <- sort(unique(as.integer(phred)))

+    

+    if( (phred[1] < 0) || (max(phred) > 93) )

+        stop("Only phred values in 0:93 are allowed.")

+

+    ascii <- phred + 33

+    return(data.frame(ascii=ascii, phred=phred,

+                    char=ascii2char(ascii, multiple=TRUE)))

+}

+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

+

+# unexported functions,  do not check for x

+rel_int  <- function(x) {return(.Call("rel_int", x, PACKAGE="seqTools"))}

+rel_real <- function(x) {return(.Call("rel_real", x, PACKAGE="seqTools"))}

+

+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

+enlargeIntMat <- function(x, newDim){

+    if(!is.matrix(x))

+        stop("x must be matrix.")

+

+    if(!is.numeric(newDim))

+        stop("newDim must be numeric.")

+    

+    newDim <- as.integer(newDim)

+

+    if(length(newDim) != 2)

+        stop("newDim must have length 2.")

+

+    return(.Call("r_enlarge_int_mat", x, newDim, PACKAGE="seqTools"))

+}

+

+kMerIndex <- function(kMers, k=nchar(kMers)[1], base=1)

+{

+    if(!is.character(kMers))

+        stop("kMers must be character.")

+

+    if(!is.numeric(k))

+        stop("k must be numeric.")

+    k <- as.integer(k)

+

+    if(k<0 || k > max_k)

+        stop("k must be in range 0, ... , ", max_k, ".")

+

+    if(!all(nchar(kMers) == k))

+        stop("All kMers must have k characters!")

+

+    if(!is.numeric(base))

+        stop("base must be numeric")

+

+    if(length(base) > 1)

+        stop("base must have length 1.")

+    base<-as.integer(base)

+

+    if(!(base %in% 0:1))

+        stop("base must be 0 or 1.")

+

+    return(.Call("get_Kmer_Index", kMers, k, PACKAGE="seqTools") + base)

+}

+

+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

+

+

+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

+## END OF FILE

+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##