Back to Search
Start Over
mbImpute: an accurate and robust imputation method for microbiome data.
- Source :
-
Genome biology [Genome Biol] 2021 Jun 28; Vol. 22 (1), pp. 192. Date of Electronic Publication: 2021 Jun 28. - Publication Year :
- 2021
-
Abstract
- A critical challenge in microbiome data analysis is the existence of many non-biological zeros, which distort taxon abundance distributions, complicate data analysis, and jeopardize the reliability of scientific discoveries. To address this issue, we propose the first imputation method for microbiome data-mbImpute-to identify and recover likely non-biological zeros by borrowing information jointly from similar samples, similar taxa, and optional metadata including sample covariates and taxon phylogeny. We demonstrate that mbImpute improves the power of identifying disease-related taxa from microbiome data of type 2 diabetes and colorectal cancer, and mbImpute preserves non-zero distributions of taxa abundances.
- Subjects :
- Actinobacteria classification
Actinobacteria genetics
Actinobacteria isolation & purification
Bacteroidetes classification
Bacteroidetes genetics
Bacteroidetes isolation & purification
Case-Control Studies
Colorectal Neoplasms diagnosis
Colorectal Neoplasms pathology
Diabetes Mellitus, Type 2 diagnosis
Diabetes Mellitus, Type 2 pathology
Firmicutes classification
Firmicutes genetics
Firmicutes isolation & purification
Fusobacteria classification
Fusobacteria genetics
Fusobacteria isolation & purification
Humans
Phylogeny
Polymerase Chain Reaction methods
Proteobacteria classification
Proteobacteria genetics
Proteobacteria isolation & purification
RNA, Ribosomal, 16S genetics
Whole Genome Sequencing
Colorectal Neoplasms microbiology
DNA, Bacterial genetics
Diabetes Mellitus, Type 2 microbiology
Metagenome
Microbiota genetics
Software
Subjects
Details
- Language :
- English
- ISSN :
- 1474-760X
- Volume :
- 22
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- Genome biology
- Publication Type :
- Academic Journal
- Accession number :
- 34183041
- Full Text :
- https://doi.org/10.1186/s13059-021-02400-4