ISoLDE (version 1.0.2)

target: 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

See Also

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