Entering edit mode
After closer inspection I noticed that Reads and RPKM values for the same samples in dba.counts$peaks changes depending which score metric I use. I was not quite sure if it something that should be expected, If that is the case, than why?
My code is:
dba.count_NON_INF.Reads <- dba.count( peak.test.NONINF, peaks= GRanges_NonINF, bRemoveDuplicates = FALSE, score = DBA_SCORE_READS )dba.count_NON_INF.Reads$peaks
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Chr Start End Score RPKM Reads cRPKM cReads |
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1chr1 10014 10397 14 11.2965190 14 1 1 |
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2chr1 180723 180910 6 9.9157375 6 1 1 |
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3chr1 181437 181568 2 4.7181753 2 1 1 |
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4chr1 629102 629953 2930 1064.0289316 2930 1 1 |
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5 chr1 633374 634042 3603 1666.8755497 3603 1 1 |
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6chr1 778350 778907 72 39.9477826 72 1 1 |
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7chr1 827085 827736 30 14.2414970 30 1 1 |
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8chr1 869749 870148 13 10.0689882 13 1 1 |
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dba.count_NON_INF.RPKM <- dba.count(peak.test.NONINF, peaks= GRanges_NonINF, bRemoveDuplicates = FALSE, score = DBA_SCORE_RPKM )dba.count_NON_INF.RPKM$peaks
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Chr Start End Score RPKM Reads cRPKM cReads |
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1chr1 10014 10397 11.2965190 11.2965190 14 1 1 |
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2chr1 180723 180910 8.2631146 8.2631146 5 1 1 |
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3chr1 181437 181568 7.0772630 7.0772630 3 1 1 |
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4chr1 629102 629953 1147.5533870 1147.5533870 3160 1 1 |
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5chr1 633374 634042 1848.2286486 1848.2286486 3995 1 1 |
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6chr1 778350 778907 40.5026129 40.5026129 73 1 1 |
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7chr1 827085 827736 15.6656467 15.6656467 33 1 1 |
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8chr1 869749 870148 10.0689882 10.0689882 13 1 1 |
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Kind Regards
Lauma
