Hi
I have a dataframe of genomic positions something like below:
chr start end strand 1a 2a 3a 1b 2b 3b 1c
2c 3c 1d 2d 3d
chr1 201199522 201199523 - 51 62 63 46 53 58
53 78 37 27 65 62
chr1 201199584 201199585 - 42 49 35 54 62 55
43 56 26 21 64 63
chr1 201199603 201199604 - 45 46 55 49 41 57
45 52 26 21 62 69
chr1 201199608 201199609 - 40 45 47 63 54 50
40 45 25 22 64 63
chr1 37944086 37944087 - 100 92 96 78 74 76
76 61 65 84 100 100
chr1 37944119 37944120 - 89 95 93 81 67 76
74 51 63 100 65 100
I would like to use a kruskal test with multi-test correction, probably
from the agricolae package, on each genomic coordinate (i.e. row) to
calculate whether treatment groups a,b,c & d are different (where 1,2 & 3
would be replicates within the groups a,b,c, & d).
What is the best way to achieve this? I would have thought the options are:
i) use transform in plyr
ii) assign group numbers by genomic coordinate and treatment group and
perform the kruskal test on each genomic coordinate group
Does anyone have any suggestions to achieve this in the quickest way?
Thanks in advance
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