‹‹ Back to SVS Home

PED/TPED/BED File

[next] [prev] [prev-tail] [tail] [up]

3.4 PED/TPED/BED File

[Picture]

Figure 9: PED/TPED/BED File Import Window

SVS can import plain text PED/MAP files, plain text TPED/TFAM files, and optimized binary PED or BED files (which should have corresponding BIM/FAM files). Because these files have full marker map information for each SNP, the marker map is also imported into SVS and automatically applied to the dataset.

In the Import PED/TPED/BED File window you can select the Text PED/MAP format, the Text TPED/TFAM format, or the Binary BED/FAM/BIM format. If you select the PED/MAP format, you can browse for a PED file by clicking on Browse. A corresponding MAP file will be automatically filled in, but you may choose to browse for a different MAP file. Similarly, if you select the TPED/TFAM format, you can browse for a TPED file and the corresponding TFAM file will be automatically filled in. If you select the BED/FAM/BIM format, you can browse for a BED file and the corresponding FAM/BIM files will be automatically filled in.

For all import formats, you can specify a dataset name, but you can only specify encoding options for the PED/MAP and TPED/TFAM formats. The default is to encode missing phenotypes in the Sex or Affection Status column as “-9” and missing genotypes as “0”. If your PED, TPED, and/or TFAM file has a different encoding you can specify it in the “Missing genotype” or “Missing phenotype” fields.

The final options allow you to specify whether you are importing human genome data or non-human genome data. If you are importing non-human genome data, the number of autosomal chromosomes in the data needs to be specified.

NOTE:

  1. The first four columns of the PED, TFAM, and FAM file formats are identifiers and encode missing values with the “0” string.
  2. The Binary BED/FAM/BIM import format is only available with the Whole Genome Analysis module.

[next] [prev] [prev-tail] [front] [up]