length.ms
(Package: rtfbs) :
Length of MS object
Return number of sequences contained in MS object
● Data Source:
CranContrib
● Keywords:
● Alias: length.ms
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RTFBS can store MS objects in R's memory, or C's memory for efficency reasons. This function transforms an MS object whose data is stored in memory within R into an MS object whose data is stored in C's memory. The result is a new MS object in R whose data is stored in C memory. Copying an MS object from R into C is performed automatically by RTFBS when it needs to run C code. The user will probably not need to call this function.
● Data Source:
CranContrib
● Keywords: ms
● Alias: as.pointer.ms
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RTFBS can store MS objects in R's memory, or C's memory for efficency reasons. This function transforms an MS object whose data is stored in memory on the C side to an MS object whose data is stored on the R side. The result is a new MS object containing data stored in memory on the R side copied from memory on the C side Copying an MS object from C into R enables modification of the MS object using generic R functions. To do the reverse, (copying an MS object from R to C), use the as.pointer.ms function.
● Data Source:
CranContrib
● Keywords: ms
● Alias: from.pointer.ms
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score.ms
(Package: rtfbs) :
Score sequences against a PWM
Score all potential binding sites in an MS object. If a PWM has N rows, then score every observed N-mer in the MS object. The score is given by the log likelihood of the N-mer given the PWM, minus the log likelihood of the N-mer under the Markov model specified by mm. By default, only potential binding sites with scores > 0 are returned, but this can be modified with the threshold argument.
● Data Source:
CranContrib
● Keywords:
● Alias: score.ms
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split.ms
(Package: rtfbs) :
Split sequences
Split sequences in MS object at given locations, or based on a numeric window size. If splitting based on a numeric window size, (i.e. every 500 bases) specify the maximum number of bases per sequence in the f parameter. If splitting based on specific locations, use read.feat(FullPath) to read in a BED file specifying the locations, and use the resulting object in the f parameter.
● Data Source:
CranContrib
● Keywords:
● Alias: split.ms
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ms
(Package: rtfbs) :
Multiple Sequence (MS) Objects
Creates a new Multiple Sequences (MS) object to hold given sequences.
● Data Source:
CranContrib
● Keywords: ms
● Alias: ms
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Determine if data in MS object is stored in R (by value) or C (by reference). If data is stored in C, it can be copied to R using the function from.pointer.ms. Conversely, if the data is stored in R, it can be copied to C using the function as.pointer.ms.
● Data Source:
CranContrib
● Keywords:
● Alias: is.pointer.ms
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gcContent.ms
(Package: rtfbs) :
Get GC content of each sequence in an MS object
Get GC content of each sequence in an MS object
● Data Source:
CranContrib
● Keywords:
● Alias: gcContent.ms
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Returns list of sequences in an MS object
● Data Source:
CranContrib
● Keywords:
● Alias: sequences.ms
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print.ms
(Package: rtfbs) :
Printing MS objects
Prints an MS (multiple sequence) object. #'
● Data Source:
CranContrib
● Keywords: ms
● Alias: print.ms
●
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