File import

AnnotatedDataFrame operator

Description

Converts a RData file containing an AnnotatedDataFrame object to a Tercen dataset.

Usage
Input projection .
documentId is the documentId
Output relations .
documentId character, the id of the document
Details

An AnnotatedDataFrame consists of two parts. There is a collection of samples and the values of variables measured on those samples. There is also a description of each variable measured.

References

AnnotatedDataFrame

readRDS operator

Description

readRDS operator imports rdsdata files

Usage
Input projection .
col documentid, this the documentid of the file
Output relations .
a tercen table tableid, for every tablid there is a documentid relation
Details

The operator takes the documentIds (i.e. the RDS data file) and converts them to a tercen table.

References

see the readRDS() function in base R.

See Also

readxls_operator ##### Examples

Read excel file operator

Description
Usage
Input projection .
row is the documentId
Output relations .
Details

The operator import excel document to tercen.

References
See Also
Examples

Read FASTA operator

Description

read_fasta operator reads a FASTA file into Tercen.

Usage
Input projection .
col factor, document ID
Output relations .
name factor, sequence name
position numeric, position of amino or nucleic acid in the sequence
letter factor, letter corresponding to an amino or nucleic acid
value numeric, numeric value associated to an amino or nucleic acid
Details

This opeartor reads a FASTA file and returns a table with one row per sequence per letter. Columns correspond to the sequence name (extracted from identifier lines starting with >), position on the sequence (starting from 1 at the beginning of the sequence), the letter (corresponding to an amino or nucleic acid), and a value (corresponding to a numeric encoding of letters for visualisation purposes).

See Also

msa_operator

FCS ZIP operator

Description

Transform zipped fcs files to tercen dataset.

Usage
Input projection .
documentId is the documentId, a zip file
Output relations .
filename character, the name of the fcs file
channels numeric, one variable per channel in the fcs file
Details

Extracts a ZIP archive of fcs files and tranforms them to tercen datasets.

Flow Cytometry Standard is a data file standard for the reading and writing of data from flow cytometry experiments.

References
See Also
Examples

Read FCS operator

Description

read_fcs operator transforms FCS files to Tercen datasets.

Usage
Input projection .
documentId is the documentId
Output relations .
documentId character, the id of the document
Details

Transforms FCS files to Tercen dataset.

The Flow Cytometry Standard is a data file standard for the reading and writing of data from flow cytometry experiments.

Read GMT operator

Description

read_gmt reads a GMT file containing a gene set annotation.

Usage
Input projection .
col character, GMT document ID
Output relations .
set_name character, gene set name
set_description character, gene set description
set_genes character, gene name
Details

GMT is a standard gene set format.

STRAF to Tercen operator

Description

straf2tercen operator allows one to import STRAF input data into Tercen.

Usage
Input projection .
y-axis numeric, input data, per cell
Output relations .
median numeric, median of the input data
Details

The operator takes all the values of a cell and returns the value which is the median.The computation is done per cell. There is one value returned for each of the input cell.

References
See Also

mean_operator ##### Examples