2011年2月28日星期一

RStudio - IDE for R

RStudio:
http://www.rstudio.org/

blog of RStudio
http://blog.rstudio.org/

RStudio, an attractive and easy-for-use editor for R. It is the best one I found now.

You can download, and install it. After it is install, everything is right there for you. You do not need to face so many troubles of configuration.

http://www.rstudio.org/download/desktop

Axioms of probability - though they are simple

Axioms of probability:

1. P(A) >= 0 for any event A. (probabilities are nonnegative.)
2. P(U) = 1. (probabilities of universe = 1. some outcome occurs every time you conduct the experiment.)
3. If A and B are mutually exclusive events, then P(A U B) = P(A) + P(B). (probability is additive over disjoint events.)

The other rules of probability can be proved from the axioms.

1. P() = 0. (the empty set has zero probability.)
2. P() = 1 - P(A). (the probability of a complement of an event.)
3. P(A U B) = P(A) + P(B) - P(A N B). (the addition rule of probability.)

2011年2月27日星期日

ASA sections on: statistical computing and statistical graphics

here the biannual data expo in this site:

http://stat-computing.org/dataexpo/

PHYLOGEOVIZ: a web-based program that visualizes genetic data on maps

PHYLOGEOVIZ: plot pie chart

GO with R and Bioconductor

please refer "GO with R and Bioconductor" in

Bioconductor Digest, Vol 96, Issue 27

for GO annotation by gene name with R/bioconductor.

2011年2月26日星期六

a more powerful djvu viewer for you in Mac or others

It, DjVuLibre http://djvu.sourceforge.net/, is more powerful viewer of djvu files I have ever experienced.

You may like it.

2011年2月24日星期四

a new phrase to me - as if/as though

for example:

I was out of the office and it looks as though Juhn was too.

gedit and textWrangler with R

You could be looking for collaboration of R with text editor, here are two:

(1) gedit and R:
http://m.feng.li/r-tips

(2) textWrangler and R:
http://macsci.jelmerborst.nl/files/tag-r.php

DIA, a diagram creation program.

here, a good guide for using DIA to generate a diagram

http://plindenbaum.blogspot.com/

2011年2月23日星期三

Reproducible Research

R is armed with several tools for reproducible research.

Here, you can find the review of those tools:
http://cran.r-project.org/web/views/ReproducibleResearch.html

nonetheless and nevertheless

  • none·the·less
    • In spite of that; nevertheless

you may need to add more fonts to Adobe Illustrator

Adobe Illustrator is usually used for sharpening of scientific plotting, especially the vector plotting. It works fine the normal operations. But, some fonts missed in the default installation. So, you may need to add some.

In windows, you can copy/paste the font files in AI's installation folder, for example: /AI/Support Files/Required/Fonts

2011年2月22日星期二

tips for linux

Here are tips for Linux:

http://www.codecoffee.com/tipsforlinux/index-linux.html

How to compile & execute C programs under Linux

There are tips for compiling and executing C programs under Linux.

http://www.codecoffee.com/tipsforlinux/articles/18.html

invoking bamova in updated Mac OS system

##############################################################
1.1 download bamova for its website (http://www.uwyo.edu/buerkle/software/bamova/).
1.2 create a folder for bamova and conserved the downloaded binary for Mac OS (bamova 1.0 binary for Mac OS X (Intel-based))

# not only binary file for Mac OS in the following folder
abt6-mao-mbp:bamova jianfengmao$ ls
bamova_1.0_osx bamova_1.0_osx.tar.gz bamova_1.0_src.tar.gz bamova_manual_1.0.pdf

1.3 get the binary file compressed

##############################################################
2.1 install gsl lib, which is necessary for invoking bamova

# create a folder anywhere in your computer for gsl
/Users/jianfengmao/gsl/

# download the updated version of gsl and install it in the standard location (/usr/local)
Curl -O http://ftp.cw.net/pub/gnu/gsl/gsl-1.14.tar.gz
tar xzvf gsl-1.14.tar.gz
cd gsl-1.14
./configure
make
sudo make install # should be done by sudo mode

2.2 check if gsl was installed

abt6-mao-mbp:lib jianfengmao$ pwd
/usr/local/lib

abt6-mao-mbp:lib jianfengmao$ ls
ImageMagick-6.6.1 libgcc_s_ppc64.1.dylib libgfortran.dylib libtkstub8.4.a tkConfig.sh
gcc libgcc_s_x86_64.1.dylib libgfortran.la ppc64 x86_64
libgcc_s.1.dylib libgfortran.2.0.0.dylib libtcl8.4.dylib tcl8.4
libgcc_s.10.4.dylib libgfortran.2.dylib libtclstub8.4.a tclConfig.sh
libgcc_s.10.5.dylib libgfortran.a libtk8.4.dylib tk8.4
abt6-mao-mbp:lib jianfengmao$ ls
ImageMagick-6.6.1 libgfortran.2.0.0.dylib libgsl.dylib libtclstub8.4.a tk8.4
gcc libgfortran.2.dylib libgsl.la libtk8.4.dylib tkConfig.sh
libgcc_s.1.dylib libgfortran.a libgslcblas.0.dylib libtkstub8.4.a x86_64
libgcc_s.10.4.dylib libgfortran.dylib libgslcblas.a pkgconfig
libgcc_s.10.5.dylib libgfortran.la libgslcblas.dylib ppc64
libgcc_s_ppc64.1.dylib libgsl.0.dylib libgslcblas.la tcl8.4
libgcc_s_x86_64.1.dylib libgsl.a libtcl8.4.dylib tclConfig.sh

##############################################################
3. test bamova

abt6-mao-mbp:bamova_1.0_osx jianfengmao$ pwd
/Users/jianfengmao/programe_files/bamova/bamova_1.0_osx

abt6-mao-mbp:bamova_1.0_osx jianfengmao$ ./bamova

USAGE: ./bamova -f frequencydata [-d distancefile -g groupfile -t theta_outputfile -m ms_outputfile -p phi_outputfile]

4. It seems bamova works for me.

2011年2月21日星期一

sqlzoo - for learning SQL

sqlzoo:
http://sqlzoo.net/

SQLite:
http://www.sqlite.org/lang.html

Awk - powerful and not difficult

Here is a guide for learning Awk (http://www.grymoire.com/Unix/Awk.html).

2011年2月20日星期日

snpEff - a good tools for annotation of genomic variant data

Please see it now, snpEff (http://snpeff.sourceforge.net/).

1. Basic statistics
# chromosome length, changes and change rate
Number of sequence changes 9,253,027
Genome total length 206,667,935
Genome effective length 206,665,490
Change rate 1 change every 22 bases
Change rate details
Chromosome Length Changes Change rate
scaffold_1 33,132,539 1,359,452 24
scaffold_10 461,865 4,215 109
scaffold_100 20,959 447 46
scaffold_1000 3,807 69 55

# Changes by types
Number changes by type
Type Total Homo Hetero
SNP 8,814,428 8,814,428 0
MNP 438,599 44,803 393,796
INS 0 0 0
DEL 0 0 0
Total 9,253,027 8,859,231 393,796
SNP base changes

A C G T
A 0 419,915 911,808 742,285
C 504,241 0 253,494 1,242,615
G 1,242,598 253,782 0 505,415
T 743,247 912,385 417,592 0
Effect by type
Effect (alphabetical order) Count

29,866
DOWNSTREAM 7,645,350
INTERGENIC 1,078,923
INTRON 2,287,900
NON_SYNONYMOUS_CODING 265,461
SPLICE_SITE 5,577
START_LOST 448
STOP_GAINED 11,550
STOP_LOST 6,794
SYNONYMOUS_CODING 176,452
SYNONYMOUS_START 101
SYNONYMOUS_STOP 2,503
UPSTREAM 7,877,135
Total 19,388,060


2.
Quality:

 Max: 0
Min: 0
Average: 0.0
Median: 0
Histogram:
Values: 0
Counts: 9689284






3.
Coverage:

 Max: 27878
Min: 1
Average: 21.248097073013856
Median: 19
Histogram:
Values: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 652 653 655 656 657 658 659 660 661 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 690 691 692 693 694 695 696 697 698 699 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 717 719 720 721 722 724 725 726 727 728 729 730 731 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 758 759 760 761 762 763 764 765 766 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 816 817 818 819 820 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 846 847 849 850 851 852 853 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 877 878 879 880 881 882 883 884 885 887 888 889 890 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 911 912 913 914 915 916 917 918 920 921 922 923 924 925 926 927 928 929 930 931 932 933 935 936 937 938 939 940 941 942 943 944 945 946 948 949 950 951 952 953 955 957 958 959 960 961 962 963 964 966 967 968 969 972 974 975 976 977 978 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 998 999 1000 1002 1004 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1033 1034 1035 1036 1037 1038 1040 1041 1042 1043 1044 1045 1047 1049 1050 1051 1052 1053 1054 1055 1056 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1072 1073 1074 1075 1077 1078 1081 1082 1083 1084 1085 1086 1087 1090 1091 1092 1094 1095 1097 1098 1100 1103 1105 1106 1107 1108 1109 1110 1111 1112 1113 1115 1118 1119 1120 1121 1123 1124 1125 1126 1128 1129 1132 1135 1136 1137 1138 1140 1142 1143 1145 1146 1147 1148 1149 1150 1151 1153 1154 1155 1156 1157 1159 1161 1162 1163 1165 1168 1169 1170 1171 1173 1174 1177 1178 1179 1181 1182 1185 1186 1187 1188 1189 1190 1191 1193 1194 1195 1196 1199 1200 1201 1203 1204 1206 1207 1208 1210 1211 1212 1213 1214 1215 1216 1217 1218 1220 1221 1224 1225 1226 1229 1231 1232 1233 1235 1236 1237 1238 1239 1240 1241 1242 1245 1246 1248 1249 1250 1251 1252 1255 1256 1257 1258 1259 1261 1262 1264 1265 1267 1268 1269 1270 1271 1272 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1287 1288 1291 1294 1296 1297 1299 1300 1301 1303 1304 1306 1317 1318 1321 1322 1324 1325 1327 1331 1332 1333 1337 1339 1340 1341 1343 1346 1347 1348 1350 1351 1352 1357 1358 1359 1363 1365 1366 1367 1374 1377 1378 1379 1380 1382 1383 1388 1390 1393 1395 1396 1397 1398 1402 1404 1405 1406 1407 1409 1410 1414 1417 1419 1420 1424 1426 1430 1432 1434 1435 1436 1439 1442 1443 1445 1447 1449 1452 1454 1455 1456 1457 1459 1464 1468 1469 1470 1474 1480 1481 1482 1483 1484 1486 1488 1489 1490 1494 1496 1498 1505 1507 1508 1510 1514 1515 1522 1523 1527 1529 1531 1532 1534 1539 1541 1544 1545 1548 1552 1556 1564 1567 1569 1573 1577 1578 1580 1586 1588 1590 1591 1593 1594 1595 1596 1597 1598 1599 1601 1605 1608 1611 1615 1621 1622 1624 1625 1626 1630 1636 1639 1642 1646 1649 1650 1651 1652 1653 1655 1660 1662 1663 1664 1666 1668 1669 1670 1671 1675 1678 1681 1685 1689 1690 1693 1695 1698 1700 1704 1707 1708 1718 1728 1730 1731 1732 1733 1746 1748 1750 1751 1753 1754 1756 1758 1767 1771 1772 1773 1775 1776 1783 1786 1787 1790 1791 1794 1798 1799 1806 1811 1815 1816 1817 1819 1826 1829 1830 1831 1833 1834 1836 1843 1846 1847 1849 1860 1861 1864 1869 1870 1882 1883 1886 1887 1889 1890 1892 1899 1900 1901 1902 1904 1907 1918 1929 1936 1939 1940 1943 1944 1945 1946 1947 1949 1951 1953 1958 1961 1965 1966 1970 1973 1981 1987 1988 1991 1993 1995 2003 2010 2011 2022 2030 2032 2041 2051 2052 2055 2056 2060 2068 2076 2079 2083 2085 2090 2095 2109 2110 2112 2118 2128 2129 2130 2134 2137 2141 2144 2146 2147 2148 2152 2158 2161 2168 2175 2182 2194 2197 2202 2205 2209 2211 2212 2217 2218 2220 2236 2239 2258 2272 2273 2280 2299 2306 2307 2312 2325 2326 2334 2340 2354 2368 2370 2390 2391 2392 2402 2404 2410 2416 2422 2424 2432 2434 2439 2440 2445 2458 2468 2473 2475 2477 2479 2483 2494 2500 2519 2530 2534 2535 2537 2543 2558 2561 2563 2587 2588 2593 2598 2606 2609 2618 2619 2621 2622 2634 2639 2640 2644 2660 2663 2672 2679 2697 2700 2702 2731 2733 2751 2758 2770 2773 2779 2794 2820 2826 2828 2829 2842 2847 2849 2853 2867 2877 2888 2909 2923 2929 2937 2949 2953 2962 2972 2978 2984 2993 2996 3000 3018 3019 3024 3028 3032 3057 3073 3086 3090 3098 3102 3104 3106 3130 3135 3150 3158 3162 3165 3168 3190 3217 3218 3227 3229 3249 3251 3254 3290 3293 3318 3323 3334 3338 3343 3350 3351 3396 3400 3420 3476 3477 3488 3499 3514 3551 3559 3560 3564 3578 3581 3620 3634 3642 3646 3663 3677 3682 3697 3708 3717 3728 3733 3735 3745 3770 3778 3796 3816 3824 3856 3870 3903 3909 3918 3941 3949 3955 3959 3961 4008 4020 4037 4052 4093 4104 4111 4139 4175 4185 4190 4208 4275 4291 4299 4341 4347 4354 4366 4377 4394 4436 4445 4448 4463 4473 4493 4509 4565 4586 4587 4589 4605 4612 4615 4619 4621 4623 4624 4638 4646 4647 4671 4741 4750 4753 4772 4778 4813 4820 4883 4891 4899 4900 4903 4926 4930 4957 4958 4977 4979 4988 5021 5048 5061 5093 5198 5209 5275 5303 5387 5388 5396 5431 5499 5550 5621 5678 5723 5744 5817 5919 5933 6017 6047 6119 6128 6176 6364 6573 6603 6628 6633 6666 6739 6827 6829 6849 7071 7159 7187 7218 7240 7255 7263 7268 7347 7361 7489 7665 7690 7757 7927 7942 8014 8018 8073 8080 8126 8143 8153 8154 8180 8356 8419 8483 8754 8927 8997 9035 9082 9162 9432 9577 9631 9894 10029 10167 10287 10658 10900 10910 11335 11659 12235 12253 12389 12520 12532 12652 12656 12661 13239 13386 13596 13725 13866 13923 13974 14316 17353 20916 22727 26623 27345 27878
Counts: 260368 210290 172564 185477 217296 255784 286180 301517 299616 289012 277175 264645 257694 252625 252095 254003 257215 262327 266517 272268 276677 279122 282038 282853 278641 274726 267452 256627 243466 229557 212480 196603 178876 161222 143987 126938 111597 97664 84847 72427 62080 52861 44990 38175 32313 27225 23448 20254 17066 14929 13095 11794 10305 9085 8364 7608 6942 6329 5952 5655 5476 4994 4570 4293 4134 3809 3698 3360 3224 3048 2869 2703 2544 2323 2203 2107 1893 1927 1758 1634 1611 1523 1412 1340 1305 1245 1202 1109 1119 1109 1014 934 913 907 858 857 843 808 742 773 714 664 650 628 622 601 563 522 534 520 464 474 476 449 397 433 428 378 371 355 346 389 335 360 332 350 341 281 329 246 276 298 238 254 246 266 234 244 217 250 204 213 205 241 205 215 175 196 161 175 164 183 198 190 136 160 146 141 149 134 138 141 153 133 149 135 123 118 125 133 110 119 110 110 109 118 94 110 115 96 109 119 98 81 91 87 88 95 97 79 86 81 90 67 94 75 80 85 106 73 87 77 58 79 87 73 67 67 67 62 71 61 74 57 68 58 61 63 56 48 39 45 58 64 54 63 52 56 56 48 42 53 54 43 56 39 31 56 49 53 56 51 37 49 48 43 52 42 49 35 53 39 48 44 27 32 54 32 34 53 41 34 32 31 40 33 37 30 40 39 37 25 28 27 28 23 26 23 25 38 25 30 20 31 35 21 32 34 37 31 31 39 32 34 34 25 28 32 22 27 22 21 31 27 29 19 26 33 27 27 20 32 17 24 30 20 13 28 20 18 20 21 16 13 19 19 22 26 23 22 18 12 17 22 21 13 17 18 12 21 23 17 19 26 18 13 19 15 16 16 20 18 19 14 15 13 14 17 21 7 16 13 21 20 15 22 25 11 12 18 16 12 20 21 12 12 7 16 15 12 9 16 15 10 10 11 14 10 9 10 14 14 9 17 15 14 13 14 21 7 8 11 13 7 14 8 13 13 16 11 19 12 15 9 11 15 5 15 11 13 12 14 15 14 9 9 12 9 13 16 15 14 7 8 6 9 19 10 12 5 8 8 10 12 9 12 7 9 6 15 8 13 9 9 11 8 14 7 21 15 11 7 12 11 10 17 14 15 13 12 9 12 7 15 16 10 2 8 7 8 11 8 5 8 7 13 7 10 6 8 11 5 14 13 5 8 11 5 9 8 6 11 7 1 6 6 4 10 11 6 7 8 5 6 7 9 5 6 7 6 12 4 4 5 9 8 10 6 5 11 5 11 10 5 8 6 7 8 11 8 8 6 6 7 11 6 6 11 8 6 3 7 9 8 10 3 11 12 4 11 6 4 6 15 5 6 9 8 7 4 8 3 6 7 6 4 6 4 3 4 3 5 14 3 4 5 6 5 9 7 2 5 4 4 5 1 5 8 5 3 2 4 4 3 2 5 4 1 5 4 4 3 4 11 8 2 5 4 8 4 9 7 3 5 2 6 2 5 4 6 7 5 4 7 5 3 6 7 9 3 6 4 3 7 5 5 2 6 9 3 3 5 6 5 8 2 3 1 6 5 2 5 5 5 7 4 1 2 3 4 1 11 3 3 5 1 7 2 4 4 5 5 5 1 2 1 1 4 2 4 2 4 2 2 2 3 3 3 4 3 5 8 1 1 4 4 1 1 6 3 2 5 6 3 2 3 3 4 2 7 2 4 3 3 1 4 3 2 3 2 2 4 2 4 2 6 3 3 1 6 3 6 3 5 2 1 1 5 2 2 2 2 5 3 2 5 1 3 4 4 4 2 3 3 5 4 1 1 1 4 4 3 4 1 2 2 1 5 3 4 3 4 4 4 4 2 4 1 1 2 2 1 6 3 2 1 2 4 5 1 1 2 2 1 5 1 1 2 3 4 5 1 1 3 2 3 3 4 5 4 5 5 1 2 2 1 4 6 4 1 3 1 6 5 4 2 2 2 1 1 5 6 3 2 4 3 2 4 4 1 5 4 4 4 2 3 2 4 4 5 1 1 4 2 3 1 3 1 2 3 2 2 1 5 1 6 1 3 3 2 3 1 2 1 4 3 3 2 1 1 1 1 1 4 2 2 1 3 2 2 2 3 5 5 2 2 2 2 2 2 2 6 1 3 2 4 2 2 2 4 2 2 1 1 2 1 5 2 3 1 3 3 3 5 1 3 1 1 1 1 2 2 5 4 1 3 1 1 3 4 2 1 1 3 1 1 2 1 4 1 1 2 2 2 1 2 1 2 1 2 1 1 1 3 1 2 1 3 1 1 1 3 3 1 1 2 1 3 5 2 3 1 1 1 2 1 1 3 4 2 2 2 2 1 2 1 1 1 2 2 2 3 1 1 1 1 6 2 2 1 2 3 2 2 1 3 1 1 1 2 4 5 1 2 1 3 1 1 1 2 1 2 2 2 1 1 2 1 2 2 1 1 4 2 3 2 1 4 2 1 1 1 1 1 2 4 3 3 1 1 2 1 4 2 1 1 1 4 1 2 2 3 2 1 4 1 1 1 1 2 3 2 1 3 2 3 1 1 2 1 3 1 2 3 1 3 1 1 1 1 2 1 2 3 2 1 2 1 3 1 1 2 4 2 2 1 1 4 1 2 3 1 1 1 1 2 1 1 1 3 2 2 1 1 3 1 2 3 1 1 2 1 3 1 1 1 1 1 1 1 2 1 1 1 3 1 3 1 1 2 1 2 2 2 1 3 2 2 2 1 2 1 1 1 1 2 1 2 1 1 2 1 1 2 1 1 2 1 1 2 1 1 3 1 2 1 2 1 1 1 1 1 1 1 1 2 1 2 1 1 1 1 1 1 1 1 1 1 2 3 1 1 1 1 1 2 2 1 2 1 2 1 1 1 1 3 1 1 2 1 1 3 1 2 1 2 1 1 1 1 2 4 1 1 1 1 1 4 2 1 1 3 2 1 1 1 1 1 1 1 2 1 1 1 1 2 1 3 1 1 3 1 1 2 1 1 1 1 1 1 1 1 2 1 2 1 1 2 2 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 2 2 1 1 1 1 1 3 1 1 1 1 3 1 1 1 1 1 2 2 2 1 1 2 2 1 2 2 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 2 2 1 1 1 2 1 1 1 3 1 1 1 1 3 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 2 2 1 2 2 1 3 1 1 1 1 1 1 1 1 1 1 1 1 3 1 1 1 2 1 1 1 1 1 2 2 1 2 1 1 2 2 1 1 1 1 1 3 1 1 1 1 1 1 1 1 1 3 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 1 1 1 1 1 1 1 2 1 2 2 1 1 1 1 1 1 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1


4.

Insertions and deletions length:

 Max: -1
Min: -13
Average: -1.5641302282510652
Median: -2
Histogram:
Values: -13 -12 -11 -10 -9 -8 -7 -6 -5 -4 -3 -2 -1
Counts: 8 5 14 60 126 306 2676 7111 12711 30842 66566 184506 610815



5. Codon changes:

6.
Amino acid changes:


* A C D E F G H I K L M N P Q R S T V W Y
* 2,503
387
410
253

484 921


962 1,194 695

845 643
A
14,463
872 1,099
1,455





1,040

2,376 4,990 5,090

C 438
2,985

1,092 620







1,240 1,492

413 1,750
D
712
5,593 3,479
1,919 777



3,662




841
1,163
E 1,166 1,013
4,183 6,543
2,245

4,950



1,527


1,161

F

842

6,139

1,289
3,897




1,734
994
1,344
G 544 1,430 1,013 1,998 2,417
12,540







3,848 2,455
1,520 341
H


626


3,000

886
1,004 563 1,780 1,619



1,924
I




1,231

9,145 445 1,986 1,701 948

405 668 2,714 3,720

K 917


3,075


756 6,527
919 3,712
1,353 3,192
1,301


L 1,010



5,135
1,008 2,767
24,648 1,561
2,455 980 1,412 2,181
2,782 415
M







2,805 721 1,507 116


404
1,383 1,194

N


2,360


895 1,097 2,839

5,470


2,635 1,007

1,031
P
1,016




1,028

4,135

12,082 1,204 1,165 3,603 1,310


Q 1,985


1,405

2,204
1,746 1,204

956 4,137 2,138




R 1,879
2,074


2,720 2,237 886 3,758 1,616 594
1,028 3,134 12,122 2,137 810
1,626
S 1,088 1,702 1,818

2,582 1,653
933
3,383
2,919 2,639
1,992 19,834 3,048
286 1,345
T
3,336





3,877 1,314
1,691 1,162 982
851 2,969 13,414


V
3,716
760 819 1,358 1,116
4,971
3,238 1,466





13,925

W 1,644
606


271


569



1,156 318

35
Y 879
1,254 607
1,273
1,283



804


723


3,835

7. Changes by chromosome

Seurat - visual analystics for the integrative analysis of microarray data

Seurat, (http://seurat.r-forge.r-project.org/manual.html) for visualizing genomic data.

Bayesian areal wombling

Bayesian areal wombling (http://www.esajournals.org/doi/full/10.1890/10-0807.1) can be used for detecting the ecological boundary using areal data. I want to know if it can be used for point referenced data.

This software was created by SPH (http://www.biostat.umn.edu/rrs.php).

softwares installation in Linux

Here (http://www.wuxfiles.org/linuxhelp/softinstall.html) is a good guide for software installation in Linux.

usage of BEDTools

This webpage (http://code.google.com/p/bedtools/wiki/Usage#shuffleBed) lists usages of BEDTools, with simple examples.

spatial tips for R users

The spatial analysis (http://spatialanalysis.co.uk/) gives much good directions and hints about spatial analysis/plotting. You can find an R sections, R Spatial Tips (http://spatialanalysis.co.uk/r/).

2011年2月16日星期三

Usages of TESS - a robust spatial genetic tools

# the installation folder of TESS
jmao@-----------------------------/solexa_tools/TESS/bin$ ls
tessmV11 tessmV11BYM tessmV11noAdm

# the first one
$ ./tessmV11
Typical Usage: tessm -FF -NN -AA -LL -KK -PP -DD -SS -BB
Options can be specified in any order.

Required Options:
-FF: F = File Name of Input Data File
For file name contains spaces, input it as "F".
-NN: N = Number of Individuals
-AA: A = Ploidy (1 = Haploid, 2 = Diploid, ...)
-LL: L = Number of Loci
-KK: K = Number of Clusters
-TT: T = Degree of Trend
-PP: P = sPatial interaction parameter (default: 1.0)
-DD: D = Parameter of Dirichlet Allele Frequency Model (no F-model)
-SS: S = Total Number of Sweeps of MCMC
-BB: B = Burn In Number of Sweeps of MCMC

Optional Options:
-rr: r = Number of Extra Rows in Data File, Default: 0
-cc: c = Number of Extra Columns in Data File, Default: 0
-ii: i = Folder Name of Input Data File, Default: Current Folder
For folder name contains spaces, input it as "i".
-oo: o = Folder Name of Output Result Files, Default: Current Folder
For folder name contains spaces, input it as "o".
-pp: p = Configuration File for Continue from Highest Likelihood Run, Default: NULL
For file name contains spaces, input it as "p".
-dd: d = Number of dummy individuals, Default: 0
-uu: u = Update sigma?
u = y, Yes (Default)
u = n, No
-upup: up = Update Psi?
up = y, Yes
up = n, No (Default)
-xx: x = admiXture parameter, Default: 30.0
-mm: m = Name of file containing map (ascii-raster format) to predict admixture coefficients on (optional)
For file name contains spaces, input it as "m".
-nn: n = number of coordinates to use in regression. Default: 2.
If n = 1, the second coordinate is used. n=0 dis the same as T=0
-ss: s = Shuffle update order for MCMC?
s = y, Yes
s = n, No (Default)
-jj: j = Init the run with Neighbor Joining tree
j = y, Yes
j = n, No (Default)
-gg: g = Name of file containing Geographic distances between individuals (optional)
For file name contains spaces, input it as "g".
-scsc: sc = scale parameter for geographic distances. User predefined value or enter one. Ignored if no geographic distance file is given.
sc = m, Mean distance between individuals (default)
sc = d, meDian distance between individuals
sc = x, maX distance between individuals
sc = value of the scale parameter (e.g. 10.4)
-spsp: sp = SPecial data format: one individual = one row
sp = y, Yes
sp = n, No (Default)
-bsbs: bs = Burn-In Structure, Default: 0
jmao@oka:/ebio/abt6_projects/backup/solexa_tools/TESS/bin$ ls
tessmV11 tessmV11BYM tessmV11noAdm

# the second one
$ ./tessmV11BYM
Typical Usage: tessm -FF -NN -AA -LL -KK -PP -DD -SS -BB
Options can be specified in any order.

Required Options:
-FF: F = File Name of Input Data File
For file name contains spaces, input it as "F".
-NN: N = Number of Individuals
-AA: A = Ploidy (1 = Haploid, 2 = Diploid, ...)
-LL: L = Number of Loci
-KK: K = Number of Clusters
-TT: T = Degree of Trend
-DD: D = Parameter of Dirichlet Allele Frequency Model (no F-model)
-SS: S = Total Number of Sweeps of MCMC
-BB: B = Burn In Number of Sweeps of MCMC

Optional Options:
-rr: r = Number of Extra Rows in Data File, Default: 0
-cc: c = Number of Extra Columns in Data File, Default: 0
-ii: i = Folder Name of Input Data File, Default: Current Folder
For folder name contains spaces, input it as "i".
-oo: o = Folder Name of Output Result Files, Default: Current Folder
For folder name contains spaces, input it as "o".
-pp: p = Configuration File for Continue from Highest Likelihood Run, Default: NULL
-dd: d = Number of dummy individuals, Default: 0
For file name contains spaces, input it as "p".
-uu: u = Update sigma?
u = y, Yes (Default)
u = n, No
-xx: x = admiXture parameter, Default: 30.0
-mm: m = Name of file containing map (ascii-raster format) to predict admixture coefficients on (optional)
For file name contains spaces, input it as "m".
-ss: s = Shuffle update order for MCMC?
s = y, Yes
s = n, No (Default)
-bsbs: bs = Burn-In Structure, Default: 0
-scsc: sc = scale parameter for geographic distances. User predefined value or enter one. Ignored if no geographic distance file is given.
sc = m, Mean distance between individuals (default)
sc = d, meDian distance between individuals
sc = x, maX distance between individuals
sc = value of the scale parameter (e.g. 10.4)
-spsp: sp = SPecial data format: one individual = one row
sp = y, Yes
sp = n, No (Default)
-gg: g = Name of file containing Geographic distances between individuals (optionnal)
For file name contains spaces, input it as "g".

# the last one
$ ./tessmV11noAdm
Typical Usage: tessm -FF -NN -AA -LL -KK -PP -DD -SS -BB
Options can be specified in any order.

Required Options:
-FF: F = File Name of Input Data File
For file name contains spaces, input it as "F".
-NN: N = Number of Individuals
-AA: A = Ploidy (1 = Haploid, 2 = Diploid, ...)
-LL: L = Number of Loci
-KK: K = Number of Clusters
-PP: P = Interaction Parameter of HMRF
-DD: D = Parameter of Dirichlet Allele Frequency Model
-SS: S = Total Number of Sweeps of MCMC
-BB: B = Burn In Number of Sweeps of MCMC

Optional Options:
-rr: r = Number of Extra Rows in Data File, Default: 0
-cc: c = Number of Extra Columns in Data File, Default: 0
-dd: d = Number of Dummy Individuals, Default: 0
-ii: i = Folder Name of Input Data File, Default: Current Folder
For folder name contains spaces, input it as "i".
-jj: j = Init the run with Neighbor Joining tree
j = y, Yes
j = n, No (Default)
-oo: o = Folder Name of Output Result Files, Default: Current Folder
For folder name contains spaces, input it as "o".
-pp: p = Configuration File for Continue from Previous Run, Default: NULL
For file name contains spaces, input it as "p".
-spsp: sp = SPecial data format: one individual = one row
sp = y, Yes
sp = n, No (Default)
-gg: g = Name of file containing Geographic distances between individuals (optional)
For file name contains spaces, input it as "g".
-scsc: sc = scale parameter for geographic distances. User predefined value or enter one. Ignored if no geographic distance file is given.
sc = m, Mean distance between individuals (default)
sc = d, meDian distance between individuals
sc = x, maX distance between individuals
sc = value of the scale parameter (e.g. 10.4)