readFullDataTable: convert a GenomeStudio FullDataTable file to the import...
In fitPoly: Genotype Calling for Bi-Allelic Marker Assays
readFullDataTable R Documentation
convert a GenomeStudio FullDataTable file to the import format
for fitPoly
Description
A GenomeStudio file in wide format (samples side-by-side) is
converted to a fitPoly input file in long format
Usage
readFullDataTable(filename, rawXY=FALSE,
markergroups=list(), out, filetype=c("dat","RData")[2])
Arguments
filename
name of a FullDataTable tab-separated text file exported from
Illumina's GenomeStudio. The file must contain a column "Name" with the
marker names, and for each sample a pair of columns "sample.X" and "sample.Y"
if rawXY is FALSE, or "sample.X raw" and "sample.Y raw" (note the space)
if rawXY is TRUE. Further columns may be present but are not read.
rawXY
if FALSE (default) the normalized .X and .Y columns are read;
if TRUE the "raw" columns (.X raw and .Y raw) are read instead.
markergroups
a list with character vectors of marker names, or integer
vectors of marker numbers in file order. If the data set is large, the
conversion to long format may exceed memory limits. In these cases the data
can be split into marker groups that are converted separately and each saved
to a separate file. If the list is empty (default) all markers are converted
as one block.
out
the name of an output file (without extension). If a list of
markergroups is given, out must be a valid file name (without extension);
in that case multiple output files are created with filenames in which
the list element numbers are appended to out. If no markergroups are specified
out may also be set to "" or NA; in that case no file is created and the
converted data are only returned as function result.
If out is not "" or NA, then also a file <out>_meanR.dat is saved with for
all samples their mean R value and number of missing data (over all markers)
filetype
either "dat" or "RData" (default): the former produces
tab-separated text files, the latter saves RData files with the converted
data in a data frame with name "dat".
Details
The wide-format input is converted to a long-format form with
columns MarkerName, SampleName, X, Y, R (= X + Y) and ratio (= Y / R).
The X and Y signal intensities are obtained from the <sample>.X and <sample>.Y
columns in the input data (or from the <sample>.X raw and <sample>.Y raw
columns if rawXY is TRUE). R and ratio are calculated from these values
and not read from the input data.
Value
If no markergroups are specified, a data.frame is returned with
columns MarkerName, SampleName, X and Y (also if raw data are read, the
column names are X and Y), R (= X + Y), ratio (= Y / (X+Y) ).
If a list of markergroups is specified the function result is NULL
and the converted data.frames are only saved as files.
If the saved files are RData files, they all contain one data.frame named
"dat".
fitPoly documentation built on April 3, 2025, 8:58 p.m.
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| readFullDataTable | R Documentation |
convert a GenomeStudio FullDataTable file to the import format for fitPoly
Description
A GenomeStudio file in wide format (samples side-by-side) is converted to a fitPoly input file in long format
Usage
readFullDataTable(filename, rawXY=FALSE,
markergroups=list(), out, filetype=c("dat","RData")[2])
Arguments
filename |
name of a FullDataTable tab-separated text file exported from Illumina's GenomeStudio. The file must contain a column "Name" with the marker names, and for each sample a pair of columns "sample.X" and "sample.Y" if rawXY is FALSE, or "sample.X raw" and "sample.Y raw" (note the space) if rawXY is TRUE. Further columns may be present but are not read. |
rawXY |
if FALSE (default) the normalized .X and .Y columns are read; if TRUE the "raw" columns (.X raw and .Y raw) are read instead. |
markergroups |
a list with character vectors of marker names, or integer vectors of marker numbers in file order. If the data set is large, the conversion to long format may exceed memory limits. In these cases the data can be split into marker groups that are converted separately and each saved to a separate file. If the list is empty (default) all markers are converted as one block. |
out |
the name of an output file (without extension). If a list of
markergroups is given, out must be a valid file name (without extension);
in that case multiple output files are created with filenames in which
the list element numbers are appended to out. If no markergroups are specified
out may also be set to "" or NA; in that case no file is created and the
converted data are only returned as function result. |
filetype |
either "dat" or "RData" (default): the former produces tab-separated text files, the latter saves RData files with the converted data in a data frame with name "dat". |
Details
The wide-format input is converted to a long-format form with columns MarkerName, SampleName, X, Y, R (= X + Y) and ratio (= Y / R). The X and Y signal intensities are obtained from the <sample>.X and <sample>.Y columns in the input data (or from the <sample>.X raw and <sample>.Y raw columns if rawXY is TRUE). R and ratio are calculated from these values and not read from the input data.
Value
If no markergroups are specified, a data.frame is returned with
columns MarkerName, SampleName, X and Y (also if raw data are read, the
column names are X and Y), R (= X + Y), ratio (= Y / (X+Y) ).
If a list of markergroups is specified the function result is NULL
and the converted data.frames are only saved as files.
If the saved files are RData files, they all contain one data.frame named
"dat".
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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