R/Strains_and_Gene_Families.R
In wrightrc/r1001genomes: Access and analyze the 1001 genomes Arabidopsis resequencing dataset
### CODE INPUTS ================================================================
strains <-
c(88,108,139,159,265,350,351,403,410,424,428,430,470,476,484,504,506,531,544,
546,628,630,680,681,685,687,728,742,763,765,766,768,772,801,853,854,867,868,
870,915,932,991,992,997,1002,1006,1061,1062,1063,1066,1070,1158,1166,1254,
1257,1313,1317,1552,1612,1622,1651,1652,1676,1684,1739,1741,1756,1757,1793,
1797,1819,1820,1829,1834,1835,1851,1852,1853,1872,1890,1925,1942,1943,1954,
2016,2017,2031,2053,2057,2081,2091,2106,2108,2141,2159,2166,2171,2191,2202,
2212,2239,2240,2276,2278,2285,2286,2317,2370,2412,4779,4807,4826,4840,4857,
4884,4900,4939,4958,5023,5104,5151,5165,5210,5236,5249,5253,5276,5279,5349,
5353,5395,5486,5577,5644,5651,5717,5718,5720,5726,5741,5748,5757,5768,5772,
5776,5779,5784,5798,5800,5811,5822,5830,5831,5832,5836,5837,5856,5860,5865,
5867,5874,5890,5893,5907,5921,5950,5984,5993,6008,6009,6010,6011,6012,6013,
6016,6017,6019,6020,6021,6022,6023,6024,6025,6030,6034,6035,6036,6038,6039,
6040,6041,6042,6043,6046,6064,6069,6070,6071,6073,6074,6076,6077,6085,6086,
6087,6088,6090,6091,6092,6094,6095,6096,6097,6098,6099,6100,6101,6102,6104,
6105,6106,6107,6108,6109,6111,6112,6113,6114,6115,6118,6119,6122,6123,6124,
6125,6126,6128,6131,6132,6133,6134,6136,6137,6138,6140,6141,6142,6145,6148,
6149,6150,6151,6153,6154,6163,6166,6169,6172,6173,6174,6177,6180,6184,6188,
6189,6191,6192,6193,6194,6195,6198,6201,6202,6203,6209,6210,6214,6216,6217,
6218,6220,6221,6231,6235,6237,6238,6240,6241,6242,6243,6244,6252,6255,6258,
6268,6276,6284,6296,6390,6396,6413,6424,6434,6445,6680,6739,6740,6744,6749,
6750,6805,6806,6814,6830,6897,6898,6900,6901,6903,6904,6907,6908,6909,6911,
6913,6915,6917,6918,6919,6920,6922,6923,6924,6926,6927,6929,6931,6932,6933,
6938,6940,6943,6944,6945,6951,6956,6957,6958,6959,6960,6961,6963,6966,6967,
6968,6969,6970,6971,6973,6974,6975,6976,6979,6981,6982,6984,6986,6987,6989,
6990,6992,6997,7000,7002,7003,7008,7013,7014,7025,7026,7028,7031,7033,7036,
7058,7061,7062,7063,7064,7067,7068,7071,7072,7077,7081,7092,7094,7096,7102,
7103,7106,7107,7109,7111,7117,7119,7120,7125,7126,7127,7130,7133,7138,7143,
7147,7158,7160,7161,7162,7163,7164,7165,7169,7177,7181,7183,7186,7192,7199,
7202,7203,7207,7208,7209,7213,7217,7218,7223,7231,7236,7244,7248,7250,7255,
7258,7268,7273,7276,7280,7282,7287,7288,7296,7298,7305,7306,7307,7314,7316,
7319,7320,7322,7323,7327,7328,7332,7333,7337,7342,7343,7344,7346,7347,7349,
7350,7353,7354,7356,7358,7359,7372,7373,7377,7378,7382,7383,7384,7387,7394,
7396,7404,7411,7413,7415,7416,7417,7418,7419,7424,7427,7430,7460,7461,7471,
7475,7477,7514,7515,7516,7517,7520,7521,7523,7525,7529,7530,7566,7568,7717,
7757,7767,7917,7947,8037,8057,8077,8132,8171,8214,8222,8227,8230,8231,8233,
8234,8235,8236,8237,8238,8239,8240,8241,8242,8243,8244,8246,8247,8249,8256,
8258,8259,8264,8283,8284,8285,8290,8297,8306,8307,8311,8312,8326,8334,8335,
8337,8343,8351,8354,8357,8365,8366,8369,8376,8386,8387,8419,8420,8422,8424,
8426,8427,8464,8483,8699,8723,9027,9057,9058,9067,9069,9070,9075,9078,9079,
9081,9084,9085,9089,9091,9095,9099,9100,9102,9103,9104,9105,9106,9111,9113,
9114,9115,9121,9125,9128,9130,9131,9133,9134,9298,9312,9314,9321,9323,9332,
9336,9339,9343,9352,9353,9363,9369,9370,9371,9380,9381,9382,9383,9386,9388,
9390,9391,9392,9394,9395,9399,9402,9404,9405,9407,9408,9409,9412,9413,9416,
9421,9427,9433,9436,9437,9442,9450,9451,9452,9453,9454,9455,9470,9471,9476,
9481,9503,9506,9507,9508,9509,9510,9511,9512,9513,9514,9515,9517,9518,9519,
9520,9521,9522,9523,9524,9525,9526,9527,9528,9529,9530,9531,9532,9533,9534,
9535,9536,9537,9539,9540,9541,9542,9543,9544,9545,9546,9547,9548,9549,9550,
9551,9552,9553,9554,9555,9556,9557,9558,9559,9560,9561,9562,9564,9565,9567,
9568,9569,9571,9573,9574,9576,9577,9578,9579,9581,9582,9583,9584,9585,9586,
9587,9588,9589,9590,9591,9592,9593,9594,9595,9596,9597,9598,9599,9600,9601,
9602,9606,9607,9608,9609,9610,9611,9612,9613,9615,9616,9617,9619,9620,9621,
9622,9624,9625,9626,9627,9628,9629,9630,9631,9632,9633,9634,9635,9636,9637,
9638,9639,9640,9641,9642,9643,9644,9645,9646,9647,9648,9649,9651,9653,9655,
9656,9657,9658,9659,9660,9661,9663,9664,9665,9666,9667,9668,9669,9670,9671,
9672,9673,9676,9677,9678,9679,9680,9681,9682,9683,9684,9685,9686,9687,9689,
9690,9691,9692,9693,9694,9695,9696,9697,9698,9699,9700,9701,9703,9704,9705,
9706,9707,9708,9709,9710,9711,9712,9713,9714,9716,9717,9718,9719,9720,9721,
9722,9723,9725,9726,9727,9728,9729,9730,9731,9732,9733,9735,9736,9737,9738,
9739,9741,9743,9744,9745,9747,9748,9749,9754,9755,9756,9757,9758,9759,9761,
9762,9764,9766,9768,9769,9770,9771,9772,9774,9775,9776,9777,9778,9779,9780,
9781,9782,9783,9784,9785,9786,9787,9788,9789,9790,9791,9792,9793,9794,9795,
9796,9797,9798,9799,9800,9801,9802,9803,9804,9805,9806,9807,9808,9809,9810,
9811,9812,9813,9814,9815,9816,9817,9819,9820,9821,9822,9823,9824,9825,9826,
9827,9828,9830,9831,9832,9833,9834,9835,9836,9837,9838,9839,9840,9841,9843,
9844,9845,9846,9847,9848,9849,9850,9851,9852,9853,9854,9855,9856,9857,9858,
9859,9860,9861,9862,9864,9866,9867,9868,9869,9870,9871,9873,9874,9875,9876,
9877,9878,9879,9880,9881,9882,9883,9885,9886,9887,9888,9890,9891,9892,9894,
9895,9897,9898,9899,9900,9901,9902,9903,9904,9905,9906,9908,9909,9910,9911,
9912,9914,9915,9917,9918,9920,9921,9924,9925,9926,9927,9928,9929,9930,9932,
9933,9935,9937,9938,9939,9941,9942,9943,9944,9945,9946,9947,9948,9949,9950,
9951,9952,9953,9955,9956,9957,9958,9959,9960,9962,9963,9964,9965,9966,9968,
9969,9970,9971,9972,9973,9974,9975,9976,9978,9979,9980,9981,9982,9983,9984,
9985,9986,9987,9988,9990,9991,9993,9995,9996,9997,9998,9999,10001,10002,
10004,10005,10006,10008,10009,10010,10011,10012,10013,10014,10015,10017,
10018,10020,10022,10023,10027,14312,14313,14314,14315,14318,14319,15560,
15591,15592,15593,18694,18696,19949,19950,19951)
# save(strains, file = "data/strains.RData")
ARFgenes <- genes <- c("AT3G62980",
"AT4G03190",
"AT3G26810",
"AT1G12820",
"AT4G24390",
"AT5G49980",
"AT2G39940")
IAAgenes <- c("AT4G14560",
"AT3G23030",
"AT1G04240",
"AT5G43700",
"AT1G15580",
"AT1G52830",
"AT3G23050",
"AT2G22670",
"AT5G65670",
"AT1G04100",
"AT4G28640",
"AT1G04550",
"AT2G33310",
"AT4G14550",
"AT1G80390",
"AT3G04730",
"AT1G04250",
"AT1G51950",
"AT3G15540",
"AT2G46990",
"AT3G16500",
"AT4G29080",
"AT5G25890",
"AT4G32280",
"AT3G62100",
"AT3G17600",
"AT2G01200",
"AT5G57420",
"AT1G15050")
TPLgenes <- c("AT1G15750",
"AT1G80490",
"AT3G16830",
"AT5G27030",
"AT3G15880")
wrightrc/r1001genomes documentation built on Nov. 10, 2019, 12:45 p.m.
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### CODE INPUTS ================================================================
strains <-
c(88,108,139,159,265,350,351,403,410,424,428,430,470,476,484,504,506,531,544,
546,628,630,680,681,685,687,728,742,763,765,766,768,772,801,853,854,867,868,
870,915,932,991,992,997,1002,1006,1061,1062,1063,1066,1070,1158,1166,1254,
1257,1313,1317,1552,1612,1622,1651,1652,1676,1684,1739,1741,1756,1757,1793,
1797,1819,1820,1829,1834,1835,1851,1852,1853,1872,1890,1925,1942,1943,1954,
2016,2017,2031,2053,2057,2081,2091,2106,2108,2141,2159,2166,2171,2191,2202,
2212,2239,2240,2276,2278,2285,2286,2317,2370,2412,4779,4807,4826,4840,4857,
4884,4900,4939,4958,5023,5104,5151,5165,5210,5236,5249,5253,5276,5279,5349,
5353,5395,5486,5577,5644,5651,5717,5718,5720,5726,5741,5748,5757,5768,5772,
5776,5779,5784,5798,5800,5811,5822,5830,5831,5832,5836,5837,5856,5860,5865,
5867,5874,5890,5893,5907,5921,5950,5984,5993,6008,6009,6010,6011,6012,6013,
6016,6017,6019,6020,6021,6022,6023,6024,6025,6030,6034,6035,6036,6038,6039,
6040,6041,6042,6043,6046,6064,6069,6070,6071,6073,6074,6076,6077,6085,6086,
6087,6088,6090,6091,6092,6094,6095,6096,6097,6098,6099,6100,6101,6102,6104,
6105,6106,6107,6108,6109,6111,6112,6113,6114,6115,6118,6119,6122,6123,6124,
6125,6126,6128,6131,6132,6133,6134,6136,6137,6138,6140,6141,6142,6145,6148,
6149,6150,6151,6153,6154,6163,6166,6169,6172,6173,6174,6177,6180,6184,6188,
6189,6191,6192,6193,6194,6195,6198,6201,6202,6203,6209,6210,6214,6216,6217,
6218,6220,6221,6231,6235,6237,6238,6240,6241,6242,6243,6244,6252,6255,6258,
6268,6276,6284,6296,6390,6396,6413,6424,6434,6445,6680,6739,6740,6744,6749,
6750,6805,6806,6814,6830,6897,6898,6900,6901,6903,6904,6907,6908,6909,6911,
6913,6915,6917,6918,6919,6920,6922,6923,6924,6926,6927,6929,6931,6932,6933,
6938,6940,6943,6944,6945,6951,6956,6957,6958,6959,6960,6961,6963,6966,6967,
6968,6969,6970,6971,6973,6974,6975,6976,6979,6981,6982,6984,6986,6987,6989,
6990,6992,6997,7000,7002,7003,7008,7013,7014,7025,7026,7028,7031,7033,7036,
7058,7061,7062,7063,7064,7067,7068,7071,7072,7077,7081,7092,7094,7096,7102,
7103,7106,7107,7109,7111,7117,7119,7120,7125,7126,7127,7130,7133,7138,7143,
7147,7158,7160,7161,7162,7163,7164,7165,7169,7177,7181,7183,7186,7192,7199,
7202,7203,7207,7208,7209,7213,7217,7218,7223,7231,7236,7244,7248,7250,7255,
7258,7268,7273,7276,7280,7282,7287,7288,7296,7298,7305,7306,7307,7314,7316,
7319,7320,7322,7323,7327,7328,7332,7333,7337,7342,7343,7344,7346,7347,7349,
7350,7353,7354,7356,7358,7359,7372,7373,7377,7378,7382,7383,7384,7387,7394,
7396,7404,7411,7413,7415,7416,7417,7418,7419,7424,7427,7430,7460,7461,7471,
7475,7477,7514,7515,7516,7517,7520,7521,7523,7525,7529,7530,7566,7568,7717,
7757,7767,7917,7947,8037,8057,8077,8132,8171,8214,8222,8227,8230,8231,8233,
8234,8235,8236,8237,8238,8239,8240,8241,8242,8243,8244,8246,8247,8249,8256,
8258,8259,8264,8283,8284,8285,8290,8297,8306,8307,8311,8312,8326,8334,8335,
8337,8343,8351,8354,8357,8365,8366,8369,8376,8386,8387,8419,8420,8422,8424,
8426,8427,8464,8483,8699,8723,9027,9057,9058,9067,9069,9070,9075,9078,9079,
9081,9084,9085,9089,9091,9095,9099,9100,9102,9103,9104,9105,9106,9111,9113,
9114,9115,9121,9125,9128,9130,9131,9133,9134,9298,9312,9314,9321,9323,9332,
9336,9339,9343,9352,9353,9363,9369,9370,9371,9380,9381,9382,9383,9386,9388,
9390,9391,9392,9394,9395,9399,9402,9404,9405,9407,9408,9409,9412,9413,9416,
9421,9427,9433,9436,9437,9442,9450,9451,9452,9453,9454,9455,9470,9471,9476,
9481,9503,9506,9507,9508,9509,9510,9511,9512,9513,9514,9515,9517,9518,9519,
9520,9521,9522,9523,9524,9525,9526,9527,9528,9529,9530,9531,9532,9533,9534,
9535,9536,9537,9539,9540,9541,9542,9543,9544,9545,9546,9547,9548,9549,9550,
9551,9552,9553,9554,9555,9556,9557,9558,9559,9560,9561,9562,9564,9565,9567,
9568,9569,9571,9573,9574,9576,9577,9578,9579,9581,9582,9583,9584,9585,9586,
9587,9588,9589,9590,9591,9592,9593,9594,9595,9596,9597,9598,9599,9600,9601,
9602,9606,9607,9608,9609,9610,9611,9612,9613,9615,9616,9617,9619,9620,9621,
9622,9624,9625,9626,9627,9628,9629,9630,9631,9632,9633,9634,9635,9636,9637,
9638,9639,9640,9641,9642,9643,9644,9645,9646,9647,9648,9649,9651,9653,9655,
9656,9657,9658,9659,9660,9661,9663,9664,9665,9666,9667,9668,9669,9670,9671,
9672,9673,9676,9677,9678,9679,9680,9681,9682,9683,9684,9685,9686,9687,9689,
9690,9691,9692,9693,9694,9695,9696,9697,9698,9699,9700,9701,9703,9704,9705,
9706,9707,9708,9709,9710,9711,9712,9713,9714,9716,9717,9718,9719,9720,9721,
9722,9723,9725,9726,9727,9728,9729,9730,9731,9732,9733,9735,9736,9737,9738,
9739,9741,9743,9744,9745,9747,9748,9749,9754,9755,9756,9757,9758,9759,9761,
9762,9764,9766,9768,9769,9770,9771,9772,9774,9775,9776,9777,9778,9779,9780,
9781,9782,9783,9784,9785,9786,9787,9788,9789,9790,9791,9792,9793,9794,9795,
9796,9797,9798,9799,9800,9801,9802,9803,9804,9805,9806,9807,9808,9809,9810,
9811,9812,9813,9814,9815,9816,9817,9819,9820,9821,9822,9823,9824,9825,9826,
9827,9828,9830,9831,9832,9833,9834,9835,9836,9837,9838,9839,9840,9841,9843,
9844,9845,9846,9847,9848,9849,9850,9851,9852,9853,9854,9855,9856,9857,9858,
9859,9860,9861,9862,9864,9866,9867,9868,9869,9870,9871,9873,9874,9875,9876,
9877,9878,9879,9880,9881,9882,9883,9885,9886,9887,9888,9890,9891,9892,9894,
9895,9897,9898,9899,9900,9901,9902,9903,9904,9905,9906,9908,9909,9910,9911,
9912,9914,9915,9917,9918,9920,9921,9924,9925,9926,9927,9928,9929,9930,9932,
9933,9935,9937,9938,9939,9941,9942,9943,9944,9945,9946,9947,9948,9949,9950,
9951,9952,9953,9955,9956,9957,9958,9959,9960,9962,9963,9964,9965,9966,9968,
9969,9970,9971,9972,9973,9974,9975,9976,9978,9979,9980,9981,9982,9983,9984,
9985,9986,9987,9988,9990,9991,9993,9995,9996,9997,9998,9999,10001,10002,
10004,10005,10006,10008,10009,10010,10011,10012,10013,10014,10015,10017,
10018,10020,10022,10023,10027,14312,14313,14314,14315,14318,14319,15560,
15591,15592,15593,18694,18696,19949,19950,19951)
# save(strains, file = "data/strains.RData")
ARFgenes <- genes <- c("AT3G62980",
"AT4G03190",
"AT3G26810",
"AT1G12820",
"AT4G24390",
"AT5G49980",
"AT2G39940")
IAAgenes <- c("AT4G14560",
"AT3G23030",
"AT1G04240",
"AT5G43700",
"AT1G15580",
"AT1G52830",
"AT3G23050",
"AT2G22670",
"AT5G65670",
"AT1G04100",
"AT4G28640",
"AT1G04550",
"AT2G33310",
"AT4G14550",
"AT1G80390",
"AT3G04730",
"AT1G04250",
"AT1G51950",
"AT3G15540",
"AT2G46990",
"AT3G16500",
"AT4G29080",
"AT5G25890",
"AT4G32280",
"AT3G62100",
"AT3G17600",
"AT2G01200",
"AT5G57420",
"AT1G15050")
TPLgenes <- c("AT1G15750",
"AT1G80490",
"AT3G16830",
"AT5G27030",
"AT3G15880")
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