filterList

This function aims to apply a given filter-citerium, a matrix or vector of <code>FALSE/TRUE</code> which is typically combined with a second layer 
which filters for a min content of filer-passing values per line for the first/main criterium.
Then all lines concerned will be removed. This will be done for all list-elements (of appropriate size) of the input-list 
(while maintaining the list-structure in the output) not matching the filtering criteria.

The efficient treatment and convenient analysis of experimental high-throughput (omics) data gets facilitated through this collection of diverse functions.
Several functions address advanced object-conversions, like manipulating lists of lists or lists of arrays, reorganizing lists to arrays or into separate vectors, merging of multiple entries, etc.
Another set of functions provides speed-optimized calculation of standard deviation (sd), coefficient of variance (CV) or standard error of the mean (SEM)
for data in matrixes or means per line with respect to additional grouping (eg n groups of replicates).
A group of functions facilitate dealing with non-redundant information, by indexing unique, adding counters to redundant or eliminating lines with respect redundancy in a given reference-column, etc.
Help is provided to identify very closely matching numeric values to generate (partial) distance matrixes for very big data in a memory efficient manner or to reduce the complexity of large data-sets by combining very close values.
Other functions help aligning a matrix or data.frame to a reference using partial matching or to mine an experimental setup to extract patterns of replicate samples.
Many times large experimental datasets need some additional filtering, adequate functions are provided.
Convenient data normalization is supported in various different modes, parameter estimation via permutations or boot-strap as well as flexible testing of multiple pair-wise combinations using the framework of 'limma' is provided, too.
Batch reading (or writing) of sets of files and combining data to arrays is supported, too.

Wolfgang Raffelsberger

wrMisc

Analyze Experimental High-Throughput (Omics) Data

filterList function

<dl><dt>lst</dt>
<dd>(list) main input, each vector, matrix or data.frame in this list will be filtered if its length or number of lines fits to <code>filt</code></dd>
<dt>filt</dt>
<dd>(logical) vector of <code>FALSE/TRUE</code> to use for filtering. If this a matrix is given, the value of <code>minLineRatio</code> will be applied as threshod of min content of <code>TRUE</code> for each line of <code>filt</code></dd>
<dt>minLineRatio</dt>
<dd>(numeric) in case <code>filt</code> is a matrix of <code>FALSE/TRUE</code>, this value will be used as threshold of min content of <code>TRUE</code> for each line of <code>filt</code></dd>
<dt>silent</dt>
<dd>(logical) suppress messages</dd>
<dt>callFrom</dt>
<dd>(character) allow easier tracking of message(s) produced</dd></dl>

Arguments

Filter for unique elements — filterList

<dl>

<dt>lst</dt>
<dd>(list) main input, each vector, matrix or data.frame in this list will be filtered if its length or number of lines fits to <code>filt</code></dd>


<dt>filt</dt>
<dd>(logical) vector of <code>FALSE/TRUE</code> to use for filtering. If this a matrix is given, the value of <code>minLineRatio</code> will be applied as threshod of min content of <code>TRUE</code> for each line of <code>filt</code></dd>


<dt>minLineRatio</dt>
<dd>(numeric) in case <code>filt</code> is a matrix of <code>FALSE/TRUE</code>, this value will be used as threshold of min content of <code>TRUE</code> for each line of <code>filt</code></dd>


<dt>silent</dt>
<dd>(logical) suppress messages</dd>


<dt>callFrom</dt>
<dd>(character) allow easier tracking of message(s) produced</dd>

</dl>

filterList: Filter for unique elements

Description

Usage

Value

Arguments

See Also

Examples