readBpmap {affxparser} | R Documentation |
Parses (parts of) a Bpmap (binary probe mapping) file from Affymetrix.
readBpmap(filename, seqIndices = NULL, readProbeSeq = TRUE, readSeqInfo = TRUE, readPMXY = TRUE, readMMXY = TRUE, readStartPos = TRUE, readCenterPos = FALSE, readStrand = TRUE, readMatchScore = FALSE, readProbeLength = FALSE, verbose = 0) readBpmapHeader(filename) readBpmapSeqinfo(filename, seqIndices = NULL, verbose = 0)
filename |
The filename as a character. |
seqIndices |
A vector of integers, detailing the indices of the
sequences being read. If NULL , the entire file is being read. |
readProbeSeq |
|
readSeqInfo |
Do we read the sequence information (a list containing information such as sequence name, number of hits etc.) |
readPMXY |
Do we read the (x,y) coordinates of the PM-probes. |
readMMXY |
Do we read the (x,y) coordinates of the MM-probes (only relevant if the file has MM information) |
readStartPos |
Do we read the start position of the probes. |
readCenterPos |
Do we return the start position of the probes. |
readStrand |
Do we return the strand of the hits. |
readMatchScore |
Do we return the matchscore. |
readProbeLength |
Doe we return the probelength. |
verbose |
How verbose do we want to be. |
readBpmap
reads a BPMAP file, which is a binary file containing
information about a given probe's location in a sequence.
Here sequence means some kind of reference sequence, typically a
chromosome or a scaffold. readBpmapHeader
reads the header of
the BPMAP file, and readBpmapSeqinfo
reads the sequence info of
the sequences (so this function is merely a convinience function).
For readBpmap
: A list of lists, one list for every sequence
read. The components of
the sequence lists, depends on the argument of the function call. For
readBpmapheader
a list with two components version
and
numSequences
. For readBpmapSeqinfo
a list of lists
containing the sequence info.
Kasper Daniel Hansen <khansen@stat.berkeley.edu>
tpmap2bpmap
for information on how to write
Bpmap files.