Matching up two vectors in R
I have two vectors in R as shown below. The first one represents amino acid numbers with some positions missing while the second one represents the full list. I need to somehow get a matched index but when I try the below I have no success.
which(PDBRenum.3V5Q[,2]==PDBXPoly.3V5Q[[1]][,3])
The data is below. Notice that the top array jumps from 544 to 551. Thus for position 16 in the top array, I need it to return position 22 in the bottom array. Thank you for your help!
> PDBRenum.3V5Q[,2]
[1] 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567
[33] 568 569 570 571 572 573 574 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601
[65] 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
[97] 634 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680
[129] 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 703 704 705 706 707 708 709 710 711 730 731 732
[161] 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764
[193] 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796
[225] 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828
[257] 829 830 831 832
> PDBXPoly.3V5Q[[1]][,3]
[1] 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
[33] 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
[65] 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
[97] 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657
[129] 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689
[161] 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 726 727 728 729 730 731 732 733 734 735
[193] 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767
[225] 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799
[257] 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831
[289] 832
Solution 1:
Use match:
match(PDBRenum.3V5Q[,2], PDBXPoly.3V5Q[[1]][,3])
With match(x,y), the ith element of the output is the first index of y that matches x[i], unless x[i] doesn't appear in y, in which case it gives NA.
match is most useful when y has no repeated values.
For example:
> match( c(1,3,5), c(2,6,7,3,1) )
[1] 5 4 NA
> match( c(1,3,5), c(2,6,7,3,1, 8,1,3) )
[1] 5 4 NA
Solution 2:
to return the indices use %in%
> (a <- letters[1:5])
[1] "a" "b" "c" "d" "e"
> b <- c("a", "b", "e", "f")
> (which(a%in%b))
[1] 1 2 5
> (which(b%in%a))
[1] 1 2 3