An object of class
Sam represents a ‘*.sam’ file. This is
supposed to be an opaque object for use by other functions. The size of a
sam object is limited to only what can be read into memory and
manipulated, which is probably at best about 1/3 of the total memory on the
system (due to R functions being "copy by value".) No support is provided
for ‘*.bam’ files.
A *.sam file name.
Parse optional sam file read tags into columns. True by default, but increases processing time a factor of 4 or so. If false will have only one "tags" column with a single tab-delimited string.
A sam object is composed of three parts, a
SamSource data. These parts can
be extracted as objects of the same name by constructor functions of the same
name applied to the
Sam object. Any function that works when applied
to a component object will work on the
Sam object too.
An object of class Sam.
1 2 3 4 5 6 7 8
## Not run: samObj <- Sam( 'myFile.sam' ) myHeader <- samHeader(samObj) myReads <- samReads(samObj) mySource <- samSource(samObj) ## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.