Mercurial > repos > davidvanzessen > report_clonality_tcell_igg

comparison RScript.r @ 4:0748ef4d42d3 draft

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author davidvanzessen
date Thu, 15 May 2014 10:00:20 -0400
parents b850200d4335
children fb219dfdcc15
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3:b850200d4335 4:0748ef4d42d3
104 } else if (locus == "tra"){ 104 } else if (locus == "tra"){
105 V = c("v.name\tchr.orderVTRAV1-1\t1\nTRAV1-2\t2\nTRAV2\t3\nTRAV3\t4\nTRAV4\t5\nTRAV5\t6\nTRAV6\t7\nTRAV7\t8\nTRAV8-1\t9\nTRAV9-1\t10\nTRAV10\t11\nTRAV12-1\t12\nTRAV8-2\t13\nTRAV8-3\t14\nTRAV13-1\t15\nTRAV12-2\t16\nTRAV8-4\t17\nTRAV13-2\t18\nTRAV14/DV4\t19\nTRAV9-2\t20\nTRAV12-3\t21\nTRAV8-6\t22\nTRAV16\t23\nTRAV17\t24\nTRAV18\t25\nTRAV19\t26\nTRAV20\t27\nTRAV21\t28\nTRAV22\t29\nTRAV23/DV6\t30\nTRAV24\t31\nTRAV25\t32\nTRAV26-1\t33\nTRAV27\t34\nTRAV29/DV5\t35\nTRAV30\t36\nTRAV26-2\t37\nTRAV34\t38\nTRAV35\t39\nTRAV36/DV7\t40\nTRAV38-1\t41\nTRAV38-2/DV8\t42\nTRAV39\t43\nTRAV40\t44\nTRAV41\t45\n") 105 V = c("v.name\tchr.orderVTRAV1-1\t1\nTRAV1-2\t2\nTRAV2\t3\nTRAV3\t4\nTRAV4\t5\nTRAV5\t6\nTRAV6\t7\nTRAV7\t8\nTRAV8-1\t9\nTRAV9-1\t10\nTRAV10\t11\nTRAV12-1\t12\nTRAV8-2\t13\nTRAV8-3\t14\nTRAV13-1\t15\nTRAV12-2\t16\nTRAV8-4\t17\nTRAV13-2\t18\nTRAV14/DV4\t19\nTRAV9-2\t20\nTRAV12-3\t21\nTRAV8-6\t22\nTRAV16\t23\nTRAV17\t24\nTRAV18\t25\nTRAV19\t26\nTRAV20\t27\nTRAV21\t28\nTRAV22\t29\nTRAV23/DV6\t30\nTRAV24\t31\nTRAV25\t32\nTRAV26-1\t33\nTRAV27\t34\nTRAV29/DV5\t35\nTRAV30\t36\nTRAV26-2\t37\nTRAV34\t38\nTRAV35\t39\nTRAV36/DV7\t40\nTRAV38-1\t41\nTRAV38-2/DV8\t42\nTRAV39\t43\nTRAV40\t44\nTRAV41\t45\n")
106 D = c("v.name\tchr.orderD\n") 106 D = c("v.name\tchr.orderD\n")
107 J = c("v.name\tchr.orderJ\nTRAJ57\t1\nTRAJ56\t2\nTRAJ54\t3\nTRAJ53\t4\nTRAJ52\t5\nTRAJ50\t6\nTRAJ49\t7\nTRAJ48\t8\nTRAJ47\t9\nTRAJ46\t10\nTRAJ45\t11\nTRAJ44\t12\nTRAJ43\t13\nTRAJ42\t14\nTRAJ41\t15\nTRAJ40\t16\nTRAJ39\t17\nTRAJ38\t18\nTRAJ37\t19\nTRAJ36\t20\nTRAJ34\t21\nTRAJ33\t22\nTRAJ32\t23\nTRAJ31\t24\nTRAJ30\t25\nTRAJ29\t26\nTRAJ28\t27\nTRAJ27\t28\nTRAJ26\t29\nTRAJ24\t30\nTRAJ23\t31\nTRAJ22\t32\nTRAJ21\t33\nTRAJ20\t34\nTRAJ18\t35\nTRAJ17\t36\nTRAJ16\t37\nTRAJ15\t38\nTRAJ14\t39\nTRAJ13\t40\nTRAJ12\t41\nTRAJ11\t42\nTRAJ10\t43\nTRAJ9\t44\nTRAJ8\t45\nTRAJ7\t46\nTRAJ6\t47\nTRAJ5\t48\nTRAJ4\t49\nTRAJ3\t50") 107 J = c("v.name\tchr.orderJ\nTRAJ57\t1\nTRAJ56\t2\nTRAJ54\t3\nTRAJ53\t4\nTRAJ52\t5\nTRAJ50\t6\nTRAJ49\t7\nTRAJ48\t8\nTRAJ47\t9\nTRAJ46\t10\nTRAJ45\t11\nTRAJ44\t12\nTRAJ43\t13\nTRAJ42\t14\nTRAJ41\t15\nTRAJ40\t16\nTRAJ39\t17\nTRAJ38\t18\nTRAJ37\t19\nTRAJ36\t20\nTRAJ34\t21\nTRAJ33\t22\nTRAJ32\t23\nTRAJ31\t24\nTRAJ30\t25\nTRAJ29\t26\nTRAJ28\t27\nTRAJ27\t28\nTRAJ26\t29\nTRAJ24\t30\nTRAJ23\t31\nTRAJ22\t32\nTRAJ21\t33\nTRAJ20\t34\nTRAJ18\t35\nTRAJ17\t36\nTRAJ16\t37\nTRAJ15\t38\nTRAJ14\t39\nTRAJ13\t40\nTRAJ12\t41\nTRAJ11\t42\nTRAJ10\t43\nTRAJ9\t44\nTRAJ8\t45\nTRAJ7\t46\nTRAJ6\t47\nTRAJ5\t48\nTRAJ4\t49\nTRAJ3\t50")
108 } else if (locus == "trg"){ 108 } else if (locus == "trg"){
109 cat("human trg not yet implemented") 109 V = c("v.name\tchr.orderV\nTRGV9\t1\nTRGV8\t2\nTRGV5\t3\nTRGV4\t4\nTRGV3\t5\nTRGV2\t6")
110 D = c("v.name\tchr.orderD\n")
111 J = c("v.name\tchr.orderJ\nTRGJ2\t1\nTRGJP2\t2\nTRGJ1\t3\nTRGJP1\t4")
110 } else if (locus == "trd"){ 112 } else if (locus == "trd"){
111 cat("human trd not yet implemented") 113 V = c("v.name\tchr.orderV\nTRDV1\t1\nTRDV2\t2\nTRDV3\t3")
114 D = c("v.name\tchr.orderD\nTRDD1\t1\nTRDD2\t2\nTRDD3\t3")
115 J = c("v.name\tchr.orderJ\nTRDJ1\t1\nTRDJ4\t2\nTRDJ2\t3\nTRDJ3\t4")
112 } 116 }
113 } else if (species == "mouse"){ 117 } else if (species == "mouse"){
114 if(locus == "trb"){ 118 if(locus == "trb"){
115 cat("mouse trb not yet implemented") 119 cat("mouse trb not yet implemented")
116 } else if (locus == "tra"){ 120 } else if (locus == "tra"){