I can not move in my work being weak in statistics I hope to find help once again on github !!!
I have a set of two COGs functions with the number of occurrences for the same species. the first represent the annotation of the total genom and the second are sequences involved in the production of a substance
my goal is to make a comparison between the two by an enrichment test
not having any knowledge in statistics I did some research and I found the fisher extract test with R
is fisher extract test adequate for the test I want and for my data?
Could someone help me with the approach to take with this test, I found some commands to use on R but the tables are only composed of 2 colomns and 2 lignes, I have more data then 2*2
my data:
COG_category | totalGenom | sequences_candidates
none | 4824 | 240
A | 555 | 9
B | 188 | 3
C | 925 | 5
D | 290 | 8
E | 687 | 12
F | 211 | 3
G | 589 | 9
H | 311 | 1
I | 463 | 6
J | 622 | 5
K | 746 | 38
L | 1189 | 23
M | 263 | 10
N | 12 | 0
O | 1351 | 49
P | 888 | 9
Q | 486 | 21
S | 3702 | 94
T | 1561 | 98
U | 678 | 27
V | 127 | 11
W | 17 | 4
Y | 30 | 0
Z | 210 | 4
Hello everyone,
I can not move in my work being weak in statistics I hope to find help once again on github !!!
I have a set of two COGs functions with the number of occurrences for the same species. the first represent the annotation of the total genom and the second are sequences involved in the production of a substance
my goal is to make a comparison between the two by an enrichment test
not having any knowledge in statistics I did some research and I found the fisher extract test with R is fisher extract test adequate for the test I want and for my data? Could someone help me with the approach to take with this test, I found some commands to use on R but the tables are only composed of 2 colomns and 2 lignes, I have more data then 2*2 my data:
COG_category | totalGenom | sequences_candidates none | 4824 | 240 A | 555 | 9 B | 188 | 3 C | 925 | 5 D | 290 | 8 E | 687 | 12 F | 211 | 3 G | 589 | 9 H | 311 | 1 I | 463 | 6 J | 622 | 5 K | 746 | 38 L | 1189 | 23 M | 263 | 10 N | 12 | 0 O | 1351 | 49 P | 888 | 9 Q | 486 | 21 S | 3702 | 94 T | 1561 | 98 U | 678 | 27 V | 127 | 11 W | 17 | 4 Y | 30 | 0 Z | 210 | 4
thanks in advance cheers