2.6 Format converter
iPat not only provides a format-free environment for genomic studies, it also allows users to utilize the build-in converter to convert files for other further purposes. By providing a genotype file and a map file (if applicable) that meet a certain format, iPat can convert them into numerical-encoded genotypes or PLINK format that is compatible to other software.
Other than specifying requested formats and arguments for quality controls, users can decide whether they would like to have missing values filled as heterozygous genotypes. Also, the argument “Batch size” determines how many samples are read into the memory at a time. The larger the batch size is, the faster the conversion would be. However, for those computing units with limited memory resources, it’s highly recommended to start from a smaller number such as 64 or 32. Large batch size will crash the program easily when dealing with a large number of markers.
## Column 1 ['V1'] of item 2 is missing in item 1. Use fill=TRUE to fill with NA (NULL for list columns), or use.names=FALSE to ignore column names. use.names='check' (default from v1.12.2) emits this message and proceeds as if use.names=FALSE for backwards compatibility. See news item 5 in v1.12.2 for options to control this message.
## Column 1 ['V1'] of item 2 is missing in item 1. Use fill=TRUE to fill with NA (NULL for list columns), or use.names=FALSE to ignore column names. use.names='check' (default from v1.12.2) emits this message and proceeds as if use.names=FALSE for backwards compatibility. See news item 5 in v1.12.2 for options to control this message.
## Column 1 ['V1'] of item 2 is missing in item 1. Use fill=TRUE to fill with NA (NULL for list columns), or use.names=FALSE to ignore column names. use.names='check' (default from v1.12.2) emits this message and proceeds as if use.names=FALSE for backwards compatibility. See news item 5 in v1.12.2 for options to control this message.
## Column 1 ['V1'] of item 2 is missing in item 1. Use fill=TRUE to fill with NA (NULL for list columns), or use.names=FALSE to ignore column names. use.names='check' (default from v1.12.2) emits this message and proceeds as if use.names=FALSE for backwards compatibility. See news item 5 in v1.12.2 for options to control this message.
## Column 1 ['V1'] of item 2 is missing in item 1. Use fill=TRUE to fill with NA (NULL for list columns), or use.names=FALSE to ignore column names. use.names='check' (default from v1.12.2) emits this message and proceeds as if use.names=FALSE for backwards compatibility. See news item 5 in v1.12.2 for options to control this message.
## Column 1 ['V1'] of item 2 is missing in item 1. Use fill=TRUE to fill with NA (NULL for list columns), or use.names=FALSE to ignore column names. use.names='check' (default from v1.12.2) emits this message and proceeds as if use.names=FALSE for backwards compatibility. See news item 5 in v1.12.2 for options to control this message.| Arguments | Default | Options |
|---|---|---|
| Input formats | None | Numerical, Hapmap, VCF, PLINK |
| Output formats | None | Numerical, PLINK |
| By missing rate | 0.2 | 0, 0.05, 0.1, 0.2, 0.5 |
| By MAF | 0.05 | 0, 0.01, 0.05, 0.1, 0.2 |
| Fill NA | unchecked | checked, unchecked |
| Batch size | 64 | 32, 64, 128, 256, 512 |