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quantable (version 0.3.6)

Streamline Descriptive Analysis of Quantitative Data Matrices

Description

Methods which streamline the descriptive analysis of quantitative matrices. Matrix columns are samples while rows are features i.e. proteins, genes. Includes methods for visualization (e.g. Heatmaps, Volcanos, pairwise QQ, Bland-Altman plot), summary statistics (e.g. CV), data normalization methods (e.g. robustscale). Read function for Progenesis.

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Install

install.packages('quantable')

Monthly Downloads

35

Version

0.3.6

License

GPL-3

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Repository

https://github.com/protViz/quantable

Maintainer

Witold Wolski

Last Published

May 15th, 2018

Functions in quantable (0.3.6)

robust scaling uses median an mad instead of mean and row applies the scaling to the columns (samples) by default

determine best Accuracy cuttoff

multigroupFCDATA

example data from multigroup analysis

geometric coefficient of variation (CV for log transformed data) Typically used to create and violin plot

normal pairs plot with different pch and plus abline

get p-values using fishers exact test for count data

Copy of http://stackoverflow.com/questions/20977477/how-to-assign-a-specific-color-to-na-in-an-image-plot

getWRValuesForVolcano

get p-values of wilcoxon rank sum test for volcano

reads file exportet from progenesis ProgenesisRead

heatmap2 facade

get NR of NA's per matrix or data.frame column

distance among matrix columns with freely choosable distance function

imageWithLabels

image plot with labels

Removes rows with more than thresh NA's from matrix

compute CV for each row in matrix

running robust scaling of arefw

getBlueWhiteRed

create blue white red palette

converts sparse representation to dense where row and col can be character vectors

pvalues for correlation matrix -

jackknifeMatrix

Compute correlation matrix with jack

filterSignificant

filters significant values and returns them as list of data.frames

addSpecialProteins

add special labels

pairsplot of QQ plots

removeDecorrelated

remove decorrelated rows

imageColorscale

if you need an colorscale to you imagelables use this

sums top rows of matrix uses median of row to determine row order

ProgenesisBuildAnnotation

build annotation from column names

Streamline descriptive analysis of quantitative data matrices

splits names and creates a matrix

correlation panel for pairs plot function (used as default in mypairsSmooth)

scale data given group

multigroupVolcano

plot volcano given multiple conditions

smoothScatter pairs

create green color scale

create divergent palette

write table in tab delimited no quotes no row.names (usefull for exporting i.e. list of foldchanges) uses write.table TODO : validate if not redundant with other write functions

unpivot data matrix

onesamplegreaterT

One sample single sided t-test on matrix

write vectors as single column table (usefull for exporting i.e. protein id's) uses write.table

imageWithLabelsNoLayout

image plot with labels

getTValuesForVolcano

get p-values of t-test values for volcano

setdiff_data.frame

setdiff for data frames

create red color scale

altman-bland plot

create density plots of cases and controls and ROC plot

xxx_replace_xxx

replace patterns (vector) with replacements (vector) in string or string vector. uses gsub and perl=TRUE taken from https://stackoverflow.com/questions/26676045

get NR of NA's per matrix or data.frame row

matrix_to_tibble

Matrix to tibble (taken from tidyquant)

histogram panel for pairs function (used as default in mypairsSmooth)

running function (default median absolute deviation)

plotOneSideVolcano

Plot and filter data coming from one sample single sided t-test

Volcano with more control

DEPRECATED Volcano plot using ggplot and ggrepel

running total ion count scaling (TIC)

get values of upper triangle from matrix

copute jack knive

create blue color scale