write_pcl: Reading, writing and annotation files

In jeitziner/TTMap: Two-Tier Mapper: a clustering tool based on topological data analysis

Description

Reading (read_pcl), writing (write_pcl) files and annotating matrices (mat2pcl)

Usage

    mat2pcl(mat, tag)
    write_pcl(df, dataname, fileaddress = "")
    read_pcl(filename, na.type = "", Nrows = -1, 
    Comment.char = "", ...)

Arguments

df	PCL object to be saved
dataname	Name of the file
fileaddress	Where to save the file
filename	File name to be loaded on R
na.type	feels the parameter na.strings of read.table
Nrows	Number of rows to be ignored (nrows of read.table)
Comment.char	comment.char of read.table
...	other read.table arguments
mat	matrix to be changed in annotated
tag	annotation

Details

The file (called filename) MUST contain 3 columns before the actual values, which are called CLID, NAME and GWEIGHT, described bellow. The first row must be the header of the columns (starting with CLID,NAME and GWEIGHT) and the second row must be EWEIGHT. Representing how much weight each column has: if some columns are n replicates they can have each a weight of 1/n.

Value

Data frame composed of

CLID	Column called CLID which is the ID of the features, which will then be the rownames of the dataframe
NAME	A possibly longer name, more meaningfull than CLID, text format
GWEIGHT	A weight for each gene or feature. If some genes are less important than others or only a pathway should be selected than the file (called filename) should have this information
Matrix	The matrix with numbers of the different observations

Author(s)

Rachel Jeitziner

See Also

control_adjustment

Examples

    library(airway)
    data(airway)
    airway <- airway[rowSums(assay(airway))>80,]
    assay(airway) <- log(assay(airway)+1,2)
    ALPHA <- 1
    to_be_saved <- TTMap::make_matrices(airway,
    seq_len(4), seq_len(4) + 4,
    rownames(airway), rownames(airway))
    TTMap::write_pcl(to_be_saved, "tempfile()", getwd())

jeitziner/TTMap documentation built on May 23, 2019, 4:24 p.m.