SRMA: an R package for resequencing array data analysis
- Details
- Publication Year 2012-07-15,Volume 28,Issue #14,Page 1928-1930
- Journal Title
- BIOINFORMATICS
- Publication Type
- Journal Article
- Abstract
- Sequencing by hybridization to oligonucleotides has evolved into an inexpensive, reliable and fast technology for targeted sequencing. Hundreds of human genes can now be sequenced within a day using a single hybridization to a resequencing microarray. However, several issues inherent to these arrays (e. g. cross-hybridization, variable probe/target affinity) cause sequencing errors and have prevented more widespread applications. We developed an R package for resequencing microarray data analysis that integrates a novel statistical algorithm, sequence robust multiarray analysis (SRMA), for rare variant detection with high sensitivity (false negative rate, FNR 5%) and accuracy (false positive rate, FPR 1 x 10(-5)). The SRMA package consists of five modules for quality control, data normalization, single array analysis, multi-array analysis and output analysis. The entire workflow is efficient and identifies rare DNA single nucleotide variations and structural changes such as gene deletions with high accuracy and sensitivity.
- Publisher
- OXFORD UNIV PRESS
- Keywords
- VARIANTS
- Research Division(s)
- Bioinformatics
- Publisher's Version
- https://doi.org/10.1093/bioinformatics/bts286
- Open Access at Publisher's Site
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3389772/- Terms of Use/Rights Notice
- Copyright © The Author 2012. Published by Oxford University Press.
Creation Date: 2012-07-15 12:00:00