Description Arguments Details Value Author(s) References See Also Examples
QUBIC
is a name short for QUalitative BIClustering algorithm, that can solve the biclustering problem in a more general form.
The fuction qubic
is the main function of the package. It calculates the bicluster in a data matrix, and it also discrete in a data matrix.
results = qubic(data, ...);
data |
Data matrix. |
file |
-file shoud be a string. The filename you want the QUBIC to write to. |
q |
-q should be (0, 0.5]. Use quantile discretization for continuous data. |
c |
-c should be (0.5, 1]. Consistency level of the block (0.5-1.0], the minimum ratio between the number of identical valid symbols in a column and the total number of rows in the output. |
f |
-f should be [0, 1.0]. Filtering overlapping blocks. |
k |
-k should be >= 2. Minimum column width of the block. |
r |
-r should be a number. The number of ranks as which we treat the up(down)-regulated value when discretization. |
o |
-o should be a number. Number of blocks to report. |
d |
-d should be either ("True", "False"). Discrete data, where user should send their processed data to different value classes, see above. |
results = qubic(data, file = "rQUBIC", q = 0.06, c = 0.95, f = 1, k = 2, r = 1, o = 100, d = "F");
The R function, qubic
returns an object of list
:
Discrete | The discrete data of your given matrix. |
ROWS_COLS | The rows and cols of the discrete data. |
BC | The number of genes and conditions of every bicluster. |
WriteToFile | The filename you have writen to. |
ArgumentList | The parameters you have given to. |
The R function, qubic
writes servel files to your Working Directory
, being the same as the C-code QUBIC does. (see details in paper)
Qin Ma (UGA) <maqin@uga.edu>
Yu Shang (JLU & UGA)<yushang@uga.edu>
Ying Xu (JLU & UGA) <xyn@bmb.uga.edu>
Maintainer: Yu Shang (JLU & UGA)<yushang@uga.edu>
Li, Ma, et al. (2009) QUBIC: a qualitative biclustering algorithm for analyses of gene expression data Nucleic Acids Research 07/2009 37(15):e101
https://code.google.com/p/qubic-biclustering/
Zhou, Ma, et al. (2012) QServer: a biclustering server for prediction and assessment of co-expressed gene clusters PLoS ONE 01/2012 7(3):e32660
QUBIC-package
getBC-method
data
toy
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | data(data);
# load the example matrix
results = qubic(data);
# run QUBIC with default parameters
# results is a variable of list with,
# the discrete data itself,
# the rows and cols of discrete data,
# the filename you want the QUBIC to write the results to,
# the argument list you sent to the QUBIC,
# the more details of results, you will see in your Working Directory,
# the name of that is what you sent to QUBIC (DEFAULT "rQUBIC"),
thisBC = getBC(results, numBC = 1);
# get the gene and condiction names of the biggest, the 1st bicluster.
results = qubic(data, file = "AnotherExample");
# QUBIC will writing to your Working Directory with "AnotherExample" as file name
results = qubic(data, file = "Example", q = 0.06, c = 0.95, f = 1, k = 2, r = 1, o = 100, d = "F");
# run QUBIC with full parameters
data(toy);
# load a discrete data named toy
results = qubic(toy, file = "toy", d = "T");
# run qubic to deal with the discrete data
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