SffHeader contains meta-data stored in the header of the SFF files read in.
Objects from this class are the result of
or from the result of
readSff. The resulting object will
header slot which is a list. If multiple sff files
were processed by either of the above functions, this list will contain
meta-data about each of these files in corresponding positions in the list.
Meta-data included is defined in the SFF file specifications and include:
The name of the file that was read in.
779314790, which encodes the string ".sff"
An optional field which indicates the position of a read index within the file.
An optional field which indicates the length of a read index within the file.
Stores the number of reads in the file.
The number of bytes required by header fields.
The length of the key sequence used for these reads.
The number of flows carried out during sequencing of the reads.
Indicates the format of the flowgram encoding. Currently "1" is the only valid value.
Indicates the nucleotide bases used for each sequencing flow.
Nucleotide sequence use for these reads.
Object of class
data frames or lists of data frames summarizing a description
of the SFF files.
signature(object = "SffHeader"): access the
header slot of
object, returning a list object.
Matt Settles <[email protected]>
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showClass("SffHeader") ## The readSffHeader can be used to extract header information from one or more sff files: sffFiles = c(system.file("extdata", "SmallTorrentTest.sff", package = "rSFFreader"), system.file("extdata","Small454Test.sff",package="rSFFreader")) header <- readSffHeader(sffFiles) header header(header)[]$number_of_reads header(header)[]$number_of_reads ## Header information is also retrieved when using readSff: sff <- readSff(sffFiles) ## Number of flows for dataset 1 and 2: header(sff)[]$number_of_flows_per_read header(sff)[]$number_of_flows_per_read
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