Description Usage Arguments Details Value Author(s)
genoQC
takes genotype data in GenABEL gwaa format and performs quality control and PCA analysis.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
gwaa |
gwaa object from GenABEL |
projectfolder |
character containing path to output folder (will be generated if not existing). |
projectname |
character used as suffix for output files. |
trait.name |
character indicating column name with trait of interest in pheno data of |
trait.type |
character with data type "gaussian" or "binomial" of |
export.genofile |
character or character vector with type(s) of QC-purified ped file to export into |
p.level.hwe |
numeric cut-off p-value for HWE in check.markers. For first round of QC it is rcommended to
skip p-level cut-off, i.e. set |
hwe.id.subset |
Subset for HWE checks in check.markers (default means controls only
if |
maf |
numeric cut off for minor allele frequency to be used in check.markers. |
checkX |
boolean. If TRUE, X-errors in |
PCA |
boolean. IF TRUE, PCA analysis performed with genotype data. |
maxCenters |
numeric with maximum count of reported clustering center if PCA is performed. |
... |
further parameter submitted to GenABEL's check.marker() function. See |
The check.marker-function from GenABEL package is used for quality control of genotype data.
It is recommended to perform two round of quality control: first QC, remove samples with different genetic
substructure, second QC. Principal component analysis for detection of genetic substructure is done
if PCA
= TRUE. The first 10 principal components are added to the covariates of the gwaa
object.
Samples are assigned to clusters and colored accordingly in PCA plots. Sample assignment is done for
up to maxCenters
cluster centers. All cluster sample lists are stored in a subfolder "ClusterLists".
The QC-purified gwaa object may be exported to PLINK-compatible file formats.
list containing two objects. First the QC-purified GenABEL gwaa object whith all samples
removed as recomended. Second an object of class check.marker containing the quality control information.
Intermediary results and plots are stored in projectfolder
as side effects.
Frank Ruehle
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.