You can perform Allelic Association Tests here.
SNPs are taken one by one. For every SNP, a 2x2 contingency table is built
by counting the number of times each possible allele SNP appears in a case
or control Sample.
Then you need to select the values defining cases and controls:
Samples with values other than the ones declared here will be
discarded and not used in the process.
When more than two possible values exist in a field. You may want to
enter only one of these values in either the "Case" or the "Control"
boxes, leaving the other box untouched (that is, leaving the "[Select
Item]" option there). By doing so, those samples that match your
explicit selection are being defined as, say, Cases (or Controls, if you
selected so). All the remaining samples having other values will be
used as the other option (Controls, in this example).
If a blank is selected " ", that means that there are Samples with no
value in the field and that those are being selected as a case or
control.
- Fisher's Exact Test.
Performs Fisher's Exact Test upon the contingency table in addition to
the Chi-square test that is always done. A combo box allows the user
to select weather to do it for every SNP or only in those cases in which
the Chi-square test has Validity=N (See below).
- Add P-Value Graph.
Creates a set of Graphical Plots of chi-square P-values ordered in
different chromosomes that shows regions of significant association
along the genome. A cluster detecting method based on the
aggregation of significantly associated SNPs will soon be added.
- Odds Ratio - Haldane Correction.
If some value of the original contingency table is 0, this option tells
SNPator to perform the Haldane Correction when computing Odds
Ratios and their Confidence Intervals.
- Logistic Regression.
The association value can be adjusted by some of the fields in the samples table using logistic regression. Results from logistic
regression association test will be collected in a different file from
the rest of the analysis. The following restrictions are applied in the
regression process in order to avoid inconsistent results when dealing
with incomplete data:
Fields with only one value in all the selected samples will be
excluded from the regression.
For each SNP, a case-control/allele contingency table is created
and SNPs with blanks in this table are discarded.
For each SNP and for each non-numeric adjusting field, a case-
control/field-value contingency table is created and SNPs with
blanks in this table are discarded.
Fields with numeric values are treated always as covariables
even if the original SNPator field is of categoric type.
- Batch mode.
This is a fundamental time-saving feature. Selecting one of the fields in
the Samples or SNP table, SNPator will run this analysis as many
times as different values are in that fields, using each time only those samples or SNPs that have each of the values. For instance, if you
have defined your samples in the "sex" field as "M" or "W", selecting
"sex" as the attribute of the Sample batch mode will result in having
two runs of the analysis, taking separately men and women.
If you select at the same time sample and SNP batch fields, you are
going to obtain as many runs of the analysis as all possible
combinations of the values of samples and SNPs in the fields you
selected.
Job : A_Association
Description : Analysis 34
User : advanced
Study : Pruebas_2
Request time : 2005-10-06 14:58:28
Start time : 2005-10-06 14:58:29
End time : 2005-10-06 14:58:34
Ready to use time : 2005-10-06 14:58:38
SNP pValue Major Validity Odds Ratio
CI95 Fisher
---------------- ----------- ----- -------- --------------- ------------------- -----------
rs242051 0.0805 G N
8.5294 + 0.36 - 199.49 + 0.1630
rs423285 0.3478 G Y
3.2500 0.25 - 41.91 0.5504
rs414909 0.5582 T Y
1.6667 0.30 - 9.27 0.6734
rs1342476 0.0009 ** T Y 33.0000
2.91 - 374.33 0.0028 **
rs1886340 0.0808 C Y
6.7500 0.66 - 68.78 0.1718
+ Haldane correction applied
- RS242051
| C | G | Chi Squared:
3.0545
|--------|--------| pValue: 0.0805
Case | 8 | 2 | Odds Ratio: 8.5294 +
Control | 14 | 0 | CI 95%: 0.36 - 199.49 +
|--------|--------|
- RS423285
| A | G | Chi Squared:
0.8816
|--------|--------| pValue: 0.3478
Case | 8 | 2 | Odds Ratio: 3.2500
Control | 13 | 1 | CI 95%: 0.25 - 41.91
|--------|--------|
- RS414909
| C | T | Chi Squared:
0.3429
|--------|--------| pValue: 0.5582
Case | 6 | 4 | Odds Ratio: 1.6667
Control | 10 | 4 | CI 95%: 0.30 - 9.27
|--------|--------|
- RS1342476
| C | T | Chi Squared:
10.9714
|--------|--------| pValue: 0.0009 **
Case | 1 | 9 | Odds Ratio: 33.0000
Control | 11 | 3 | CI 95%: 2.91 - 374.33
|--------|--------|
- RS1886340
| C | T | Chi Squared:
3.0483
|--------|--------| pValue: 0.0808
Case | 9 | 1 | Odds Ratio: 6.7500
Control | 8 | 6 | CI 95%: 0.66 - 68.78
|--------|--------|
At the top, you can find the usual header informing you about dates and times
of performance, user, study, filters applied and other data.
Below that, the association results are printed in several columns, containing:
- SNP
Code of the SNP
- pValue
P-value from the chi-square test applied to the 2x2 contingency
table for each SNP.
- Significance (of the chi-square test)
* for P-values<0.05, ** for P-values<0.01
- Major
The Allele positively associated with cases.
- Validity
Not valid (N) when there is some expected value in the chi-
squared contingency table that is equal or below 1.
- Odds Ratio
The Odds Ratio resulting from the association analysis of each
SNP. If the Haldane Correction has been used, the OR it is
marked with a "+" sign.
- CI95
It is the 95% Confidence Interval for the Odds Ratio value
obtained before. Here, too, if Haldane correction has been
applied it will be flagged with a "+" sign.
- Fisher_p
P-value from the Fisher exact test applied to the 2x2
contingency table for each SNP.
- Significance (of Fisher's Exact Test)
* for P-values<0.05, ** for P-values<0.01
Finally, for each SNP, ithe contingency table with some of the statistics is
printed.
- SNP
Code of the SNP.
- Major
The Allele positively associated with cases.
- Odds Ratio
The Odds Ratio equivalent coming from the Logistic
Regression coefficient.
- CI95Inf - CI95Sup
The limits of the 95% interval confidence for the Odds Ratio
value.
- pValue
In case you decided to add Graphical Plots to your analysis, you will get
a set of Graphs (one for chromosome) showing the distribution of
significance along the chromosome. In order to make visualization easier,
the plots represent -Log(P-value) against the different SNPs ordered
according to their chromosome positions.
P=0.05 and P=0.01 significance levels have been marked as horizontal
lines on the graph.