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RÓïÑÔÔÚȾɫÌåÌØÕ÷ÅԱ߻æÖÆBAMÎļþÊý¾ÝconvertBamToRle()º¯Êý-ÖÐÓ¢ÎĶÔÕÕ°ïÖúÎĵµ
By MicroRbt Martinez PhD
RÓïÑÔº¯ÊýÃû£ºconvertBamToRle()
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convertBamToRle()º¯ÊýËùÊôRÓïÑÔ°ü£ºËùÔÚR°ü¾ßÌåÃû³Æ¡¢°ü¹¦ÄܵÄÖÐÓ¢ÎÄË«ÓïÃèÊö¼ûÕýÎĺóÃæ'--ËùÔÚRÓïÑÔ°üÐÅÏ¢--'²¿·Ö¡£
ÃèÊö-----Description-----
These functions aid plotting a-la xmapbridge but in a format that is more publication friendly
ÕâЩ¹¦ÄÜÓÐÖúÓÚ»æÖÆa-la xmapbridge£¬µ«¸ñʽ¸üÒ×ÓÚ·¢²¼
ʹÓ÷½·¨-----Usage-----
# Utility MethodsUtility Methods
ʵÓ÷½·¨
convertBamToRle( bam.file.name, chr, start, end, chr.name.mapping=function( name ){ name } )
generateBridgeData( xrange, bamFiles, colours=NULL, names=NULL )
ngsTraceScale( vector.of.xbams.and.ybams )
ngsTraceLabel( rle.data )
ngsTracePlotter( rle.data, start, end, ylim, trace.label.properties=list(), smoothing.function=function( rle, ... ) { IRanges::runmean( rle, k=1001, endrule='constant' ) },
trace.clip='inherit', trace.draw.scale=FALSE, trace.bor='transparent', trace.pad=c(0,0), ... )
# Plotting MethodsPlotting Methods
»æͼ·½·¨
ngsBridgePlot( xrange, data=list(), main=NULL, sub=NULL, highlights=NULL, trace.plotter=ngsTracePlotter, genome.layout.weight=4,
trace.scale=ngsTraceScale, trace.draw.scale=NULL, trace.match.strand=TRUE, probe.plot=NULL, exon.depth.plot=genomicExonDepthPlot,
.genes=NULL, .exons=NULL, ... )
²ÎÊý-----Arguments-----
²ÎÊýbam.file.name½éÉÜ: The name of the BAM file to read in
Òª¶ÁÈ¡µÄBAMÎļþµÄÃû³Æ
²ÎÊýchr½éÉÜ: The chromosome of interest.
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²ÎÊýstart½éÉÜ: The start of the region of interest
¸ÐÐËȤÇøÓòµÄÆðµã
²ÎÊýend½éÉÜ: The end of the region of interest
¸ÐÐËȤÇøÓòµÄ¾¡Í·
²ÎÊýchr.name.mapping½éÉÜ: The function to convert between the Annmap chr name to the chr name in the BAM file. By default, this just uses chr supplied as the parameter, however it can be set to any function you like. One example of this is generalisedNameToNCBI
ÔÚAnnmap chrÃû³ÆºÍBAMÎļþÖеÄchrÃû³ÆÖ®¼äת»»µÄº¯Êý¡£Ä¬ÈÏÇé¿öÏ£¬Ëü½öʹÓÃÌṩµÄchr×÷Ϊ²ÎÊý£¬µ«ÊÇ¿ÉÒÔ½«ÆäÉèÖÃΪÄúϲ»¶µÄÈκκ¯Êý¡£ÕâÑùµÄÒ»¸öÀý×ÓÊÇgeneralisedNameToNCBI
²ÎÊýxrange½éÉÜ: The genomic range for the x-axis. Should be a GRanges object.
xÖáµÄ»ùÒò×鷶Χ¡£Ó¦¸ÃÊÇGRanges¶ÔÏó¡£
²ÎÊýbamFiles½éÉÜ: A vector containing the filenames of your BAM files.
Ò»¸ö°üº¬BAMÎļþÎļþÃûµÄÏòÁ¿¡£
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