Analyze Experimental High-Throughput (Omics) Data
Convert matrix (eg with redundant) row-names to data.frame
Convert Vector To Numeric
Check argument for Location of legend
Compare 'dat' to confindence interval of linare model 'lMod' (eg from ...
Check regression arguments
Automatic choice of colors
Avoid duplicating items between 'curNa' and 'newNa' by incrementing di...
Get M value for each group of replicates based on comp
Grow tree
row group CV (main)
Find overlap instances among range of values in lines
Get first minimum
fuse 2 instances of 3dim arr as mult cols in 3dim array
Get A value for each group of replicates
Get A value for each group of replicates based on comp
checkFileNameExtensions Function for checking file-names.
Standard Error Of Median For Each Column By Bootstrap
Add text before file-extension
Linear rescaling of numeric vertor or matrix
Adjust Value With Different Decimal Prefixes To Single Prefix Plus Uni...
Append vectors or lists, without duplcating common elements
CV of array
Organize Data as Separate List-Entries
Connect edges to from tree and extract all possible branches
cbind to non-redundant
rowCVs
Check how multiple groups of data separate or overlap based on mean +/...
Check If File Is Available For Reading
checkGrpOrder
Check order of multiple groups including non-overlapping SEM-margins
Check for similar values in series
Check for strict (ascencing or descending) order
Check For Common Unit-Name in Text
Check length of vector
Replace Most Distant Values by NA
Reorganize results of search for close (similar) values in matrix-view
Compare Means Of Two Vectors By Permutation Test
Filter for size
Transform Numeric Values To Color-Gradient
sd for each column
Planing for making all multiplicative combinations
Combine Vectors From List And Return Basic Count Statistics
Create factor-like column regrouping data regrouping simultaneaously b...
Get all combinations with TRUE from each column
Find and combine points located very close in x/y space
Combine/reduce redundant lines based on specified column
Combine Redundant Lines In List
Combine Redundant Lines In List, Deprecated
Combine replicates from list to matrix
Complete list of arrays for same dimensions
Value Matching With Option For Concatenated Terms
Confidence Interval To Given Alpha
Characterize individual contribution of single edges in tree-structure...
Convert matrix of integer to matrix of x-times repeated column-names
Assign new transparency to given colors
get coordinates of values/points in matrix according to filtering cond...
Correct vector to unique
Correct mixed slash and backslash in file path
Count from two vectors number of values close within given limits
Count same start- and end- sites of edges (or fragments)
Cut 3-dim array in list of matrixes (or arrays) similar to organizing ...
Cut character-vector at multiple sites
Cut numeric vector to n groups (ie convert to factor)
Compute matrix of differences for all pairwise combinations of numeric...
Difference in ppm between numeric values
Add letter to all elements but not last
Check Factor
Calculate ratios for each column to each column of reference-matrix
Search character-string and cut either before or after
Summarize along columns of multiple arrays in list
Summarize along columns of mult arrays in list
Convert anything to data.frame
Get series of values after last discontinuity
Bring most extreme to center
Check argument names
Check list of arrays for consistent dimensions of all arrays
Convert to simple vector (similar to unlist)
Combine annotation information from list of matrixes
Compare by distance/difference
Compare by log-ratio
Compare by PPM
Search (complementing) columns for best coverage of non-NA data for ro...
Compose sequence of (function-)calls
Convert numeric matrix to numeric
Convert/standardize names of 'query' to standard names from 'ref'
Search character-string and cut either before or after
Cut string to get all variants from given start with min and max lengt...
Model linear regression and optional plot
Extract NA-neighbour values
Extract number(s) before capital character
Extract numbers before separator followed by alphabetic character
Filter nodes & edges for extracting networks (main)This function allow...
Filter 3-dim array of numeric data (main)
Segment (1-dim vector) 'dat' into clusters
Inspect 'matr' and check if 1st line can be used/converted as header
Refine/filter 'dat1' (1dim dataset, eg cluster) with aim of keeping ce...
Remove all columns where all data are not finite
Check if vector may be numeric content
Rescale respective to specific group
Trim character string: keep only text before 'sep'
Merge Multiple Matrices (main)
find closest neighbour to numeric vector
Distances beteenw sorted points of 2-columns
Main Normalization function
Normalize columns of 2dim matrix to common linear regression fit
Return position of 'di' (numeric vector) which is most excentric (dist...
Paste-concatenate all columns of matrix
Pie plot for counting results
Add lower caps to character vector
Calculate residues of (2-dim) linear model 'lMod'-prediction of/for 'd...
Raise all values close to lowest value
Remove columns indicated by col-number
Search for (empty) columns conaining only entries defined in 'searchFi...
Replace Special Characters
row group mean (main)
row group sd (main)
row group rowSums per group (main)
Row-normalization procedure on matrix or data.frame 'dat'
Obtain normalization factor (main)
Scale between 0 and 1 (main)
Trim from end (Deprecated)
Rescale respective to specific group
Scale between min and max value (main)
Cut string to get all variants from given start with min length, depre...
Set lowest value to given value
Choose most frequent or middle of sorted vector
Reorganize array by reducing dimension 'byDim' (similar to stack() for...
Summarize columns of matrix (or data.frame) 'x' using apply (main)
Trim from start (Deprecated)
Trim From Left Side
Trim From Right Side
Check regression arguments
Convert numeric vector to matrix
Eliminate close (overlapping) points (in x & y space)
Equal character-length number
Exclude extreme values (based on distance to mean)
Normalize by adjusting exponent
Extract just one series, ie channel, of list of arrays
Extract last two numeric parts from character vector
Replacements in list
Flexible extraction of columns
Extract numeric part of matrix or data.frame
Extract specific text
Filter three-dimensional array of numeric data
Filter lines(rows) and/or columns from all suitable elements of list
Filter for unique elements
Filter nodes & edges for extracting networksThis function allows extra...
Filter for unique elements
Find close numeric values between two vectors
Find repeated elements
Find similar numeric values from two vectors/matrixes
Select groups within given range
Filter matrix to keep only first of repeated lines
Find first of repeated elements
Reduce to first occurance of repeated lines
Fuse annotation matrix to initial matrix
Fuse content of list-elements with redundant (duplicated) names
Fuse pairs to generate cluster-names
Get first of repeated by column
Print matrix-content as plot
Convert ulr-name for reading in raw-mode
Organize values into list and sort by names
Html Special Character Conversion
Extract Longest Common Text Out Of Character Vector
Transform (factor) levels into index
Test multiple starting levels for linear regression model, select best...
Fit linear regression, return parameters and p-values
Run lm on segmented data (from clustering)
rbind on lists
Make MA-List Object
Make non-redundant matrix
Match All Lines of Matrix To Reference Note
Value Matching with optional reversing of sub-parts of non-matching el...
Match names to concatenated pairs of names
Transform columns of matrix to list of vectors
Merge Multiple Matrices
Merge Multiple Matrices from List
Merge selected columns out of 2 matrix or data.frames
mergeSelCol3
Simple Multi-to-Multi Matching of (Concatenated) Terms
Fast na.omit
Merge Named Vectors
Extended version of merge for multiple objects (even without rownames)
Minimum distance/difference between values
Moderated Pair-Wise t-test From Limma
Multiple moderated pair-wise t-tests from limma
Multiple replacement of entire character elements in simple vector, ma...
Number of fragments after cut at specific character(s) within size-ran...
Number of fragments after cut at specific character(s)
Count number of non-numeric characters
Transform matrix to non-ambiguous matrix (in respect to given column)
make numeric vector non-ambiguous (ie unique)
Filter for unique elements
Non-redundant lines of matrix
Normalize Data In Various Modes
Extract pair of numeric values from vector or column-names
Order Lines of Matrix According to Reference (Character) Vector
(re)organize data of (3-dim) array as list of replicates
Simple Package Download Statistics From CRAN
Convert Pairs of Node-Names to Non-Oriented Propensity Matrix
Partial distance matrix (focus on closest)
Partial unlist of lists of lists
Advanced paste-collapse
Filter lines of matrix for max number of NAs
Filter for each group of columns for sufficient data as non-NA
Protect Special Characters
Convert p-values to lfdr
Distance of categorical data (Jaccard, Rand and adjusted Rand index)
Contingenty tables for fit of ranking
Calculate all ratios between x and y
Replace NAs by low values
Convert ratio to ppm
Read batch of csv-files
Batch Reading Of Tabulated Text-Files
Read Tabular Content Of Files With Variable Number Of Columns
Read Batch of Excel xlsx-Files
Reduce table by aggregating smaller groups
Rescaling according to reference data using linear regression.
Rescaling of multiple data-sets according to reference data using regr...
Rename columns
Reorganize matrix according to clustering-output
Search and Select Groups of Replicates
CV of replicate plates (list of matrixes)
Remove lines of matrix redundant /duplicated for 1st and 2nd column
Remove or rename enumerator tag/name (or remove entire enumerator) fro...
Remove or Reassign Orphan Indexes
Trim/Remove Redundant Words
rowSums with destinction of groups (of columns, eg groups of replicate...
Normal random number generation with close fit to expected mean and sd
rowCVs
Row group CV
rowMeans with destinction of groups (of columns, eg groups of replicat...
Count number of NAs per row and group of columns
Per line and per group sd-values
Estimate sd Of Median For Each Row By Bootstrap
Row Normalize
sd for each row (fast execution)
SEM for each row
Locate Sample Index From Index Or Name Of Pair-Wise Comparisons In Lis...
Scale data to given minimum and maxiumum
(upper) pairwise x,y combinations
Search duplicated data over multiple columns, ie pairs of data
Search Points Forming Lines At Given Slope
Simple figure showing line from start- to end-sites of edges (or fragm...
2-factorial Anova on single line of data
Sort matrix by two categorical and one integer columns
Make a list of common occurances sorted by number of repeats
Estimate Mode (Most Frequent Value)
Standardize (scale) data
Standard Eror Of Median by Boot-Strap
Summarize columns (as median,mean,min,last or other methods)
Count number of NAs per sub-set of columns
System-date (compressed format)
Print matrix-content as plot
2-Factorial Limma-Style t-Test
Make single vector gray-gradient
Locate duplicates in text and make non-redundant
Pairwise x,y combinations
Trimmed Mean
Trim redundant text
t.test on all individual values against all other values
Unify Enumerators
Report number of unique and redundant elements (optional figure)
Check for values within range of reference
Write (and convert) csv files
Express difference as ppm
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.