1. COMPASS
  2. Commit 831817a0f8263e6513372822f7a836555b1d0e13
Browse code

updated to use a csv rather than excel since readxl is throwing errors on the dev build.

gfinak authored on 07/03/2019 15:52:39
Showing 2 changed files
inst/extdata/SimpleCOMPASSExamples.csv
History View file @ 831817a
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2 
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3 
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4 
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5 
+"4","Unstimulated","SC021","IGRA+",39861,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,1,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,3,0,0,0,0,0,0,0,0,0,0,0,1,5,0,7,51,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,4,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,4,0,0,0,4,1,6,0,120,0,0,0,0,0,0,0,6,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,7,0,0,0,0,0,0,0,54,0,0,0,0,0,0,0,6,0,0,0,0,0,0,1,125,0,0,0,0,0,0,2,217,0,0,1,28,2,153,82,38950
6 
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7 
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8 
+"7","ESAT6/CFP10","SC069","IGRA+",39736,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,4,4,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,24,0,0,1,0,0,0,0,9,0,0,2,4,0,0,32,145,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,6,0,0,0,17,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5,0,0,0,2,0,0,0,115,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,15,0,0,0,0,0,0,1,125,0,0,0,0,0,0,2,24,0,0,0,0,0,0,1,309,0,0,0,2,0,0,4,789,0,1,1,21,0,2,112,37947
9 
+"8","Unstimulated","SC069","IGRA+",70022,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,1,0,0,0,1,0,1,8,174,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,3,0,0,0,35,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,2,0,0,0,1,0,1,2,283,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,3,0,0,0,0,0,0,0,129,0,0,0,0,0,0,7,10,0,0,0,0,0,0,2,159,0,0,0,2,0,0,1,110,1,0,0,28,0,2,77,68964
10 
+"9","ESAT6/CFP10","SC075","IGRA+",23472,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,5,0,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,2,0,0,0,0,0,1,0,18,0,0,0,0,1,0,0,9,1,0,0,3,6,8,12,125,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,3,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,3,0,0,0,0,0,0,0,8,0,0,0,2,0,48,2,275,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,4,0,0,0,1,0,0,0,14,0,0,0,2,0,4,0,106,0,0,0,0,0,0,0,16,0,1,0,1,1,24,3,275,0,0,0,1,0,5,1,371,0,10,0,50,16,1703,43,20276
11 
+"10","Unstimulated","SC075","IGRA+",31900,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,4,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,4,0,0,0,1,0,0,1,33,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,11,0,0,0,3,0,13,2,526,0,0,0,0,0,0,0,3,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,39,0,0,0,0,0,0,0,6,0,0,0,0,0,5,1,142,0,0,0,0,0,1,1,203,0,3,0,34,2,610,30,30202
12 
+"11","ESAT6/CFP10","SC080","IGRA+",48997,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,5,0,3,1,3,0,6,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3,0,0,0,0,0,0,0,2,0,1,0,5,7,2,6,118,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,16,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,4,0,0,1,3,0,6,3,18,0,4,7,350,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,4,0,0,0,2,0,0,0,83,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,65,0,1,0,0,1,1,7,83,4,5,14,353,3,117,96,47572
13 
+"12","UnStimulated","SC080","IGRA+",72289,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,2,0,1,0,2,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3,0,0,0,1,0,0,0,0,0,1,0,5,0,9,6,148,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,2,0,0,0,35,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,8,1,3,2,20,1,11,4,541,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,2,0,0,0,111,0,0,0,1,0,0,0,1,0,1,0,0,1,2,0,37,0,0,0,0,0,0,2,88,2,1,0,199,2,144,61,70814
14 
+"13","ESAT6/CFP10","SC184","IGRA+",75317,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,2,1,2,0,46,0,0,0,0,0,0,0,1,3,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,1,1,4,0,10,7,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,11,0,0,1,2,0,0,2,3,1,2,2,5,125,14,314,344,0,0,2,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,1,0,0,0,1,0,0,0,14,0,0,1,0,0,0,0,0,0,0,1,0,0,0,4,3,0,0,0,0,0,0,0,0,0,0,6,1,3,2,50,51,0,0,0,2,0,0,4,20,0,0,1,0,0,0,5,20,0,0,0,0,0,2,0,28,0,0,0,9,1,6,14,794,0,0,1,0,0,0,3,3,0,1,0,0,1,6,28,320,0,0,0,0,0,0,3,161,3,4,2,106,22,305,1048,71341
15 
+"14","Unstimulated","SC184","IGRA+",30055,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,4,0,0,0,0,0,0,0,2,0,0,0,0,0,15,1,152,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,30,0,0,0,0,0,0,0,5,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,3,1,0,0,1,0,0,0,109,0,0,0,0,0,0,0,2,0,1,0,0,0,3,0,102,0,0,0,0,0,0,0,30,0,3,0,37,1,166,8,29364
16 
+"15","ESAT6/CFP10","SC185","IGRA+",83570,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,2,0,0,0,0,0,3,0,3,0,61,0,59,2,0,0,0,0,0,0,0,3,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,6,0,0,0,0,0,0,1,0,0,0,0,0,1,2,2,1,0,0,0,0,0,0,0,0,3,0,2,2,281,20,167,244,0,0,2,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,3,0,0,0,12,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,6,0,0,0,0,0,0,0,0,1,0,3,2,1,0,17,78,0,0,0,3,0,0,4,13,0,0,0,0,1,0,4,14,0,0,0,0,0,0,0,15,0,0,0,10,1,2,5,488,0,0,2,0,0,0,1,6,0,1,0,2,1,8,13,244,0,0,0,0,0,1,1,204,0,7,3,128,42,352,325,80668
17 
+"16","Unstimulated","SC185","IGRA+",86897,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,6,2,2,246,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,58,0,1,0,2,0,1,0,13,0,0,0,0,0,1,0,11,0,0,0,2,0,0,1,12,0,0,0,6,1,4,0,179,0,0,0,0,0,0,0,5,0,0,0,2,0,6,0,198,0,0,0,0,0,1,0,157,2,3,1,47,9,439,46,85410
18 
+"17","ESAT6/CFP10","SC187","IGRA+",46566,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,2,0,2,0,14,2,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,3,8,0,0,0,0,0,0,0,0,0,0,0,0,0,1,2,4,0,0,0,1,0,0,1,1,2,2,3,2,60,11,179,186,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,2,0,0,1,7,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,4,0,0,0,0,0,0,0,0,1,0,4,3,0,1,10,53,0,0,0,1,0,0,0,6,0,0,0,0,0,2,2,13,0,0,0,0,0,0,0,16,0,0,0,9,3,6,5,758,0,0,0,0,0,0,1,0,0,0,0,3,1,6,10,150,0,0,0,1,0,0,1,182,0,5,6,122,17,228,271,44158
19 
+"18","Unstimulated","SC187","IGRA+",48374,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,1,0,0,0,1,0,0,0,0,0,0,1,1,4,3,7,123,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,60,0,0,0,2,0,0,0,9,0,0,0,0,0,1,0,9,0,0,0,0,0,0,0,9,0,0,0,6,0,9,1,875,0,0,0,0,0,0,0,0,0,2,0,1,0,1,0,113,0,0,0,0,0,0,0,49,0,2,0,63,2,309,28,46660
20 
+"19","ESAT6/CFP10","SC190","IGRA+",97369,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,5,2,0,0,87,2,0,0,0,0,0,0,0,2,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,1,0,0,0,1,2,0,0,12,0,0,0,0,0,0,0,0,0,0,1,0,0,2,1,0,0,0,0,1,0,0,1,1,2,0,6,7,29,10,431,341,0,0,1,3,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,4,0,0,0,34,0,0,0,0,0,0,0,0,0,0,2,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,3,7,1,3,36,263,1,0,1,0,0,0,2,11,0,0,1,0,0,0,6,7,0,0,0,0,0,0,0,32,0,0,2,11,0,4,15,1413,0,0,1,0,0,0,2,0,0,0,5,0,0,2,15,79,0,0,0,0,0,0,1,188,3,2,24,173,10,271,601,93171
21 
+"20","Unstimulated","SC190","IGRA+",90806,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,2,2,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,1,0,0,0,0,0,0,2,1,4,20,4,194,0,0,0,7,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,2,0,0,0,22,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,7,2,12,1,321,0,0,0,1,0,2,2,11,0,1,0,0,1,0,1,3,0,0,0,0,0,0,1,14,0,0,0,4,1,6,1,264,0,0,0,0,0,0,1,1,0,1,0,0,0,3,5,29,0,0,0,0,0,3,1,102,2,10,2,139,43,634,248,88648
22 
+"21","ESAT6/CFP10","SC056","EPTB",46620,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,2,0,0,27,10,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,2,0,0,0,0,0,0,0,8,0,0,0,0,0,0,0,1,0,0,0,1,0,0,5,26,0,0,0,0,0,0,0,19,0,0,0,7,0,0,172,527,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,2,0,0,0,21,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,9,0,0,2,8,0,0,12,352,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6,0,0,0,0,0,0,0,23,0,0,0,2,0,0,2,252,0,0,0,0,0,0,1,11,0,0,0,0,0,0,10,187,0,0,0,2,0,1,9,584,0,0,6,105,0,13,407,43776
23 
+"22","Unstimulated","SC056","EPTB",45440,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,1,5,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,4,0,0,0,0,0,0,1,0,0,0,0,0,0,0,12,122,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,3,0,0,0,36,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,4,0,0,0,4,0,0,1,506,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,3,0,0,0,0,0,0,0,4,1,0,0,1,0,0,1,266,0,0,0,0,0,0,0,5,0,0,0,0,0,0,0,154,0,0,0,2,0,0,0,138,0,0,2,52,0,20,63,44021
24 
+"23","ESAT6/CFP10","SC057","EPTB",36611,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,2,1,0,0,13,8,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,2,27,0,0,0,0,0,0,0,7,0,0,3,6,1,0,177,641,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,7,0,0,0,18,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,5,0,0,4,121,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,5,0,0,0,1,0,0,0,106,0,0,1,0,0,0,1,22,0,0,0,0,0,2,2,266,0,0,0,2,0,0,0,241,0,2,8,114,0,21,295,34466
25 
+"24","Unstimulated","SC057","EPTB",39992,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,6,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,1,0,0,0,1,0,0,1,129,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,13,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,7,0,0,0,0,0,1,0,208,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,6,0,0,0,1,0,0,0,137,0,0,0,0,0,0,1,8,0,0,0,0,0,0,0,109,0,0,0,0,0,0,0,107,0,0,0,52,0,24,36,39138
26 
+"25","ESAT6/CFP10","SC095","EPTB",33395,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,5,3,5,3,6,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,9,1,27,0,0,0,0,0,1,0,13,3,3,3,5,53,157,59,354,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,2,0,2,0,2,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,3,0,0,0,0,0,2,0,16,1,6,0,5,3,110,1,379,0,0,0,0,0,2,0,2,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,9,0,1,0,5,0,9,0,66,0,0,0,0,0,4,0,6,0,0,0,0,1,31,3,186,0,0,0,4,0,40,1,400,3,22,0,94,33,6218,52,24952
27 
+"26","Unstimulated","SC095","EPTB",40028,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,3,0,0,1,70,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,9,0,0,0,11,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,1,0,0,0,4,0,0,0,10,0,3,3,962,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6,0,0,0,3,0,0,0,79,0,0,0,0,0,0,0,14,0,0,0,0,0,1,0,97,0,0,0,2,0,3,1,238,0,1,0,36,2,165,53,38238
28 
+"27","ESAT6/CFP10","SC100","EPTB",39346,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,3,0,3,0,1,0,1,1,14,0,7,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,2,0,0,0,0,0,24,0,30,0,0,0,0,0,8,0,42,0,7,0,3,5,399,1,416,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,1,0,2,0,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6,0,8,0,3,0,2,5,297,1,223,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,1,0,0,0,0,0,2,2,13,0,0,0,0,0,9,0,49,1,1,0,0,1,4,1,11,0,0,0,0,0,109,1,151,0,1,1,0,4,172,4,759,0,69,2,55,91,15705,87,20512
29 
+"28","Unstimulated","SC100","EPTB",29169,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,1,0,0,0,0,0,0,1,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,2,11,0,51,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,3,0,2,0,7,0,97,6,549,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,3,0,0,0,0,0,3,0,59,0,0,0,0,0,0,2,2,0,0,0,0,1,1,1,33,0,0,0,0,0,10,2,162,1,16,0,59,35,3266,124,24643
30 
+"29","ESAT6/CFP10","SC145","EPTB",48189,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,2,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,2,0,4,14,0,7,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,5,0,4,0,0,0,0,0,0,0,0,0,0,0,0,1,21,0,26,0,0,0,0,0,1,0,0,1,9,4,4,118,431,26,471,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,1,0,1,0,0,0,1,0,1,0,0,0,5,0,8,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,2,0,1,2,1,0,0,6,68,3,53,0,0,0,2,0,5,0,2,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,3,0,4,1,2,2,46,0,66,0,0,0,0,0,6,0,9,0,0,0,0,4,163,0,127,0,0,0,0,1,22,1,37,13,64,1,48,482,18358,246,27156
31 
+"30","Unstimulated","SC145","EPTB",28248,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,4,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,1,3,67,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,8,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,2,0,0,0,1,0,0,2,67,0,0,0,4,0,0,0,8,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,17,0,0,0,1,0,0,0,49,0,0,0,0,0,0,0,12,0,0,0,0,0,1,0,47,0,0,0,1,0,0,0,35,0,0,1,18,0,108,53,27726
32 
+"31","ESAT6/CFP10","SC146","EPTB",40950,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,2,0,1,0,0,0,1,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,2,0,0,0,0,0,0,3,3,0,1,12,2,2,5,0,3,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,3,0,1,0,0,0,3,1,0,0,0,0,1,0,0,0,1,1,2,0,0,0,0,0,0,2,27,0,27,0,1,0,0,1,2,0,4,3,20,0,10,34,266,13,264,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,4,0,3,0,0,0,2,1,3,0,1,0,2,0,6,0,0,0,0,0,0,0,0,0,0,0,0,0,7,0,3,0,0,0,2,0,2,0,4,1,25,0,14,8,328,0,243,0,0,0,0,0,1,0,2,0,0,0,0,0,2,0,0,0,1,0,3,1,0,0,1,0,5,0,2,1,31,0,40,0,0,0,0,4,8,3,15,0,8,0,3,8,302,0,215,0,4,0,2,2,78,1,173,23,436,5,223,372,17237,114,20225
33 
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vignettes/SimpleCOMPASS.Rmd
History View file @ 831817a
... ... 
@@ -32,12 +32,12 @@ We need a good package to load the excel file, we'll use the tidyverse pacakge `
32 32
33 33 
 ```{r install_readxl, eval=FALSE}
34 34 
 library(BiocManager)
35 
-install.packages("readxl")
35 
+# install.packages("readxl")
36 36 
 ```
37 37
38 38 
 ```{r load_readxl}
39 39 
 library(COMPASS)
40 
-library(readxl)
40 
+# library(readxl)
41 41 
 ```
42 42
43 43 
 # Using SimpleCOMPASS
... ... 
@@ -52,14 +52,14 @@ The data used in this vignette are installed along with the `COMPASS` package, a
52 52 
 # retrieve the path to the data file in the package installation directory
53 53 
 example_data_path =
54 54 
   system.file("extdata",
55 
-              "SimpleCOMPASSExample.xlsx",
55 
+              "SimpleCOMPASSExamples.csv",
56 56 
               package = "COMPASS")
57 57 
 ```
58 58
59 59 
 With the path to the data in hand we load the file.
60 60
61 61 
 ```{r load_data}
62 
-compass_data = read_excel(example_data_path)
62 
+compass_data = read.csv(example_data_path, check.names=FALSE)
63 63 
 ```
64 64
65 65 
 ## Formatting the data
... ... 
@@ -92,7 +92,7 @@ This seems like a lot of work, but it's relatively straightforward. When using t
92 92
93 93 
 We assign the first three columns of the data set to a new `metadata` variable. These are the `PATIENT ID`, `Stimulation` and `Group` variables. We also want `metadata` to be a `data.frame` rather than a `tibble`.
94 94 
 ```{r}
95 
-metadata = compass_data[,1:3]
95 
+metadata = compass_data[,2:4]
96 96 
 metadata = as.data.frame(metadata)
97 97 
 ```
98 98
... ... 
@@ -100,7 +100,7 @@ metadata = as.data.frame(metadata)
100 100
101 101 
 ```{r}
102 102 
 # Take the remaining columns
103 
-counts = as.matrix(compass_data[,4:260])
103 
+counts = as.matrix(compass_data[,5:261])
104 104 
 dim(counts)
105 105 
 # NOTE that we still have too many columns.
106 106 
 # We should have 256, not 257.