target {ISoLDE} | R Documentation

## METADATA ABOUT THE ASR COUNT DATA.

### Description

target_file.txt: A tab-delimited file describing your input data (raw and / or normalized allele specific read (ASR) count file(s)).
Each line of the target file corresponds to a column of the `rawASRcounts` and / or
`normASRcounts` `data.frames`. Lines of target file MUST be in the same order as the columns in ASR count data. Each line contains four values, separated by a character (e.g. a tabulation) : `samples`, `parent`, `strain` and `replicate` (see the Details section for more information).
target.rda: The target_file.txt file loaded into a data.frame by the `link{readTarget}` function.

### Format

target_file.txt: A tab-delimited text file.
target.rda: A data.drame.

### Details

Details of the three columns :
`sample` : the biological sample name. A same sample name has to appear twice in the target file : one line for the maternal allele and one line for the paternal allele.
`allele` : the parental origin of the ASR count. Two possible values: `maternal` or `paternal`.
`strain` : the strain origin of the ASR count. Exactly two different values have to be provided in the whole file.
The first line of the target file has to contain these column names in the same order.
These metadata are required for both `filterT` and `isolde_test` functions.
Factice example:
sample,parent,strain
samp1,maternal,str1
samp1,paternal,str2
samp2,maternal,str1
samp2,paternal,str2
samp3,maternal,str1
samp3,paternal,str2
samp4,maternal,str1
samp4,paternal,str2

### Author(s)

Marine Rohmer marine.rohmer@mgx.cnrs.fr,
Christelle Reynès christelle.reynes@igf.cnrs.fr

### See Also

`readTarget` is a function to load into a `data.frame` and check the input target file.

[Package ISoLDE version 1.18.1 Index]