synop_dh92: Synthetic x Opata genetic map, 92 DH lines
In etnite/bwardr: Brian Ward personal R package
synop_dh92 R Documentation
Synthetic x Opata genetic map, 92 DH lines
Description
A dataframe adapted from Supplementary Dataset S7 of Gutierrez-Gonzalez et
al., 2019 containing map data on SNPs generated by a PstI-MspI double digest
genotyping-by-sequencing (GBS) protocol, with physical positions from
the International Wheat Genome Sequencing Consortium (IWGSC) v1.0
Chinese Spring wheat Reference Sequence and genetic positions derived from a
population of 92 doubled-haploid (DH) lines descended from the Synthetic x
Opata cross. Gutierrez-Gonzalez et al. performed imputation using the R
package LaByRInth (https://github.com/Dordt-Statistics-Research/LaByRInth),
which is an adaptation of the LB-Impute algorithm. Several outlier SNPs were
removed from this dataset, leaving 92,272 markers.
Usage
synop_dh92
Format
A data frame with 7,742 rows and 4 variables:
- chr
chromosome name
- id
SNP identifier
- dist
genetic position, in centiMorgans (cM)
- pos
phyiscal position, in base pairs (bp)
Details
This data is in the format required for PLINK .map files. However, note that
many programs that use PLINK files may require the header to be removed, and
may require genetic distances to be converted to Morgans.
Source
etnite/bwardr documentation built on Jan. 6, 2023, 7:12 a.m.
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| synop_dh92 | R Documentation |
Synthetic x Opata genetic map, 92 DH lines
Description
A dataframe adapted from Supplementary Dataset S7 of Gutierrez-Gonzalez et al., 2019 containing map data on SNPs generated by a PstI-MspI double digest genotyping-by-sequencing (GBS) protocol, with physical positions from the International Wheat Genome Sequencing Consortium (IWGSC) v1.0 Chinese Spring wheat Reference Sequence and genetic positions derived from a population of 92 doubled-haploid (DH) lines descended from the Synthetic x Opata cross. Gutierrez-Gonzalez et al. performed imputation using the R package LaByRInth (https://github.com/Dordt-Statistics-Research/LaByRInth), which is an adaptation of the LB-Impute algorithm. Several outlier SNPs were removed from this dataset, leaving 92,272 markers.
Usage
synop_dh92
Format
A data frame with 7,742 rows and 4 variables:
- chr
chromosome name
- id
SNP identifier
- dist
genetic position, in centiMorgans (cM)
- pos
phyiscal position, in base pairs (bp)
Details
This data is in the format required for PLINK .map files. However, note that many programs that use PLINK files may require the header to be removed, and may require genetic distances to be converted to Morgans.
Source
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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