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
GitHub link
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
GitHub link
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
GitHub link
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).
References
See Also
GitHub link
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
GitHub link
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.
GitHub link
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.
GitHub link
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