AFCHECK - winkusch/Easy2 GitHub Wiki
Check allele frequencies and strand orientation by creating an allele frequency scatter plot of each input file versus a reference.
| FUNCTION | PARAMETER | DEFAULT | DESCRIPTION |
|---|---|---|---|
| AFCHECK | --colRefFreq | Column name of the reference allele-frequency. | |
| AFCHECK | --blnWriteOutlier | TRUE | Boolean value to indicate whether outlying SNPs that differ > numLimOutlier in terms of allele frequency from the reference frequency, should be written to a separate file in the output path. Optional. Default: 1. Please use: [0 |
| AFCHECK | --blnRemoveOutlier | FALSE | Boolean value to indicate whether outlying SNPs that differ > numLimOutlier in terms of allele frequency from the reference frequency, should be excluded from the input. Optional. Default: 0. Please use: [0 |
| AFCHECK | --numLimOutlier | 0.2 | Allele frequency difference threshold that will be used to define outliers. The number of outlying SNPs will be written to the REPORT and the outlying SNPs itself will be written to a separate file in the output directory. Optional. Default: 0.2 |
| AFCHECK | --blnPlotAll | TRUE | Boolean value to indicate whether all SNPs should be plotted. If set to 0, ONLY outlying SNPs that differ > numLimOutlier in terms of allele frequency from the reference frequency, will be plotted. Optional. Default: 0 (only outlier are drawn). Please use: [0 |
| AFCHECK | --colInFreq | , | Column name of the input allele-frequency. In case the allele direction will be switched in order to match the reference alleles, this column will be adjusted for the respective SNPs by (1-colInFreq). |
| AFCHECK | --strTag | AFCHECK | Tag for the function step that will be added to related variables in the REPORT and to related output to ensure unique and easily recognizable file names and REPORT variable names. |
| AFCHECK | --strDefaultColour | INHERITED | default colour |
| AFCHECK | --numDefaultSymbol | INHERITED | defulat symbol |
| AFCHECK | --numDefaultCex | INHERITED | default cex |
| AFCHECK | --arcdColourCrit | INHERITED | array of R code expressions with criteria for varying colours |
| AFCHECK | --astrColour | INHERITED | array of colours according to criteria |
| AFCHECK | --strAxes | INHERITED | |
| AFCHECK | --strXlab | INHERITED | Plot x axis label |
| AFCHECK | --strYlab | INHERITED | Plot y axis label |
| AFCHECK | --arcdAdd2Plot | INHERITED | array of R code expressions that will be added to the plot (eg text(…)) |
| AFCHECK | --strFormat | INHERITED | graphic file format |
| AFCHECK | --rcdExclude | INHERITED | |
| AFCHECK | --numCexAxis | INHERITED | cex for axis |
| AFCHECK | --numCexLab | INHERITED | cex for lables |
| AFCHECK | --numWidth | INHERITED | Width of the plot in pixel. |
| AFCHECK | --numHeight | INHERITED | Height of the plot in pixel. |
| AFCHECK | --anumParMar | INHERITED | array of four 'par' parameters |
| AFCHECK | --anumParMgp | INHERITED | array of three 'mgp' parameters |
| AFCHECK | --strParBty | INHERITED | plot param 'bty' |
| AFCHECK | --blnGrid | INHERITED | |
| AFCHECK | --strMode | INHERITED |
Inherited parameters can be used with AFCHECK directly.
In particular, setting --fileRef at AFCHECK can be helpful if the input does not (yet) contain reference alleles and reference allele frequencies and if reference data needs to be merged from external data (this may replace an extra MERGE and ADJUSTALLELES step in the ecf-file).
If the input already contains reference alleles and reference allele frequencies there is no need to use --fileRef or any other inherited parameters.
The defined input alleles, frequency and betas will be aligned to the defined reference alleles.
Example:
AFCHECK --colInMarker ChrPosID
--colInStrand Strand
--colInA1 Effect_allele
--colInA2 Other_allele
--colInFreq EAF
--fileRef /path2reffiles/AlleleFreq_HapMap_CEU.v1.txt.gz
--acolIn ChrPosID;A1;A2;Freq1
--acolInClasses character;character;character;numeric
--colRefMarker ChrPosID
--colRefA1 A1
--colRefA2 A2
--colRefFreq Freq1
--blnMetalUseStrand 1
Output:
| REPORT VARIABLES | DESCRIPTIPON |
|---|---|
| cor__ | Pearson Correlation between the input and the reference allele frequency after aligning all directions to the reference. |
| numOutlier | Number of outlying SNPs that differ > numLimOutlier (0.2 by default) in terms of allele frequency from the reference allele frequency. |
| Checked, StrandChange, AlleleMatch, AlleleChange, n4AlleleMatch, n4AlleleChange, AlleleMismatch, AlleleInMissing, AlleleInInvalid, StrandInInvalid, AlleleRefMissing, AlleleRefInvalid, StrandRefInvalid | Inherited ADJUSTALLELES variables. Only present if --colInA1, --colInA2, --colRefA1 and --colRefA2 are used. Please see ADJUSTALLELES for a more detailed description. |
| NotInRef, NotInIn | Inherited MERGE variables. Only present if --fileRef is used. Please see MERGE for a more detailed description. |
| FILE OUTPUTS | DESCRIPTION |
|---|---|
| *.AFCHECK.[png|pdf] | Panel of allele frequency plots. |
| *.outlier.txt | If --blnWriteOutlier 1, a separate file will be written to pathOut that contains the outlying SNPs. |
| *.mismatch.txt, *. invalid.txt | Inherited ADJUSTALLELES output. Only present if --colInA1, --colInA2, --colRefA1 and --colRefA2 are used. Please see ADJUSTALLELES for a more detailed description. |
| *.notinref.txt, *.notinin.txt | Inherited MERGE output. Only present if --fileRef is used. Please see MERGE for a more detailed description. |