|
|
| (17 intermediate revisions by one other user not shown) |
| Line 1: |
Line 1: |
| | | The program is available and described on github: |
| =Download=
| |
| | |
| The program can be downloaded from github: | |
|
| |
|
| https://github.com/e-jorsboe/asaMap | | https://github.com/e-jorsboe/asaMap |
|
| |
| <pre>
| |
| git clone https://github.com/e-jorsboe/asaMap.git;
| |
| cd asaMap
| |
| make
| |
| </pre>
| |
|
| |
| So far it has only been tested on Linux systems. Use curl if you are on a MAC.
| |
|
| |
| =Example=
| |
|
| |
| This an example!!
| |
|
| |
| =Input Files=
| |
| Input files are called genotypes in the binary plink files (*.bed) format [https://www.cog-genomics.org/plink2]. And estimated admixture proportions and population specific allele frequencies. For estimating admixture proportions and population specific allele frequencies [http://software.genetics.ucla.edu/admixture/ ADMIXTURE], can be used, where .Q and .P files respectively can be given directly to asaMap.
| |
|
| |
|
| |
| A phenotype also has to be provided, this should just be text file with one line for each individual in the .fam file, sorted in the same way:
| |
|
| |
| <pre>
| |
| -0.712027291121767
| |
| -0.158413122435864
| |
| -1.77167888612947
| |
| -0.800940619551485
| |
| 0.3016297021294
| |
| ...
| |
| </pre>
| |
|
| |
| A covarite file can also be provided, where each column is a covariate and each row is an individual - should NOT have columns of 1s for intercept (intercept will be included automatically). This file has to have same number of rows as phenotype file and .fam file.
| |
|
| |
| <pre>
| |
| 0.0127096117618385 -0.0181281029917176 -0.0616739439849275 -0.0304606694443973
| |
| 0.0109944672768584 -0.0205785925514037 -0.0547523583405743 -0.0208813157640705
| |
| 0.0128395346453956 -0.0142116856067135 -0.0471689997039534 -0.0266186436009881
| |
| 0.00816783754598649 -0.0189271733933446 -0.0302259313905976 -0.0222247658768436
| |
| 0.00695928218989132 -0.0089960963981644 -0.0384886176827146 -0.012649019770168
| |
| ...
| |
| </pre>
| |
|
| |
| Example of a command of how to run asaMap with covariates included and first running ADMIXTURE:
| |
|
| |
| <pre>
| |
| #run admixture
| |
| admixture plinkFile.bed 2
| |
|
| |
| #run asaMap with admix proportions
| |
| ./asaMap -p plinkFile -o out -c $COV -y pheno.files -Q plinkFile.2.Q -f plinkFile.2.P
| |
| </pre>
| |
|
| |
| This produces a out.log logfile and a out.res with results for each site (after filtering).
| |
|
| |
| =Running asaMap=
| |
|
| |
| Example of a command of how to run asaMap with covariates included and first running ADMIXTURE:
| |
|
| |
| <pre>
| |
| #run admixture
| |
| admixture plinkFile.bed 2
| |
|
| |
| #run asaMap with admix proportions
| |
| ./asaMap -p plinkFile -o out -c $COV -y pheno.files -Q plinkFile.2.Q -f plinkFile.2.P
| |
| </pre>
| |
|
| |
| This produces a out.log logfile and a out.res with results for each site (after filtering).
| |
|
| |
|
| |
| A whole list of options can be explored by running asaMap without any input:
| |
|
| |
| <pre>
| |
| ./asaMap
| |
| </pre>
| |
|
| |
|
| |
| '''Must be specified:'''
| |
|
| |
| ; -p <filename>
| |
| Plink prefix filename of binary plink files - so without .bed/.fam/.bim suffixes.
| |
| ; -o <filename>
| |
| Output filename - a .res file will be written with the results and a .log log file.
| |
| ; -y <filename>
| |
| Phenotypes file, has to be plain text file - with as many rows as .fam file.
| |
| ; -Q <filename> (either -a or -Q)
| |
| Admixture proportions, .Q file from ADMIXTURE. Either specify this or -a.
| |
| ; -a <filename> (either -a or -Q)
| |
| Admixture proportions (for source pop1) - so first column from .Q file from ADMIXTURE. Either specify this or -Q.
| |
| ; -f <filename>
| |
| Allele frequencies, .P file from ADMIXTURE.
| |
|
| |
|
| |
| '''Optional:'''
| |
|
| |
| ; -c <filename>
| |
| Covariates, plain text file with one column for each covariates, same number of rows as .fam file. SHOULD NOT HAVE COLUMN OF 1s (for intercept) WILL BE ADDED AUTOMATICALLY!
| |
| ; -m <INT>
| |
| Model, whether an additive genotype model, or a recessive genotype model should be used (0: additive, 1: recessive - default: 0).
| |
| ; -l <INT>
| |
| Regression, whether a linear or logistic regression, should be used. Logistic regression is for binary phenotype data, linear regresion is fo quantative phenotype data. (0: linear regression, 1: logistic regression - default: 0)
| |
| ; -b <filename>
| |
| Text file containing a starting guess of the estimated coefficients.
| |
| ; -i <INT>
| |
| The maximum number of iterations to run for the EM algorithm (default: 80).
| |
| ; -t <FLOAT>
| |
| Tolerance for change in likelihood between EM iterations for finishing analysis (default: 0.0001).
| |
| ; -r <INT>
| |
| Give seed, for generation of starting values of coefficients.
| |
| ; -P <INT>
| |
| Number of threads to be used for analysis. Each thread will write to temporary file in path specified by "-o".
| |
| ; -e <INT>
| |
| Estimate standard error of coefficients (0: no, 1: yes - default: 0).
| |
| ; -w <INT>
| |
| Run M0/R0 model that models effect of other allele. Analyses are faster without having to run M0/R0. (0: no, 1: yes - default: 1)
| |
|
| |
| =Outputs=
| |
|
| |
| =Models=
| |
|
| |
| =Citation=
| |