Adaptive Normalization for miRNA Data

An adaptive normalization algorithm that selects housekeeping genes based on the sample level variability in the data. This is suitable for any data obtained from RT-qPCR assays. A manuscript describing the method is submitted to Genome Biology under ``MiRA-norm: An Adaptive Method for the Normalization of MicroRNA Array Data``, Yuda Zhu et al.


Main function of the package is miranorm. The functino will return an object containing suggest list of normalizing genes based on given dataset.

News

MiRAnorm v1.0.0 (Release date 2016-07-18)

Changes:

  • Release! Documentation of functions that are still exported are now mostly updated.

  • Fixed variable name in example for mariners to reflect dataset names.

  • Added exclude variable to exclude specific miRNA from the selection of HK genes process.

MiRAnorm v0.4.0 (Release date 2016-06-01)

Changes:

  • Include kappa agreement probabilities in final returned function. (0 if method=“simple”)

  • All adaptive normalizing genes are checked for potential treatment effect and warnings are issued if any are found. Adjusted p-values are used based on BH.

  • Small fix on treatment effect assessment for inclusion of plyr::.

  • Fixed data format issue on returned variables which returned Sample and Trt as lists.

MiRAnorm v0.3.0 (Release date 2016-04-11)

Changes:

  • Sample naming convention changed. No ‘.’ allowed in names for input data.

  • Fixed bug in norm.quant where sample names were not being passed.

  • Reconstructed ggplot output for easier read.

  • k argument no longer used. This was originally for panel breaking by CV level.

  • ggplot changed to stacked facet. Removed extraneous displays such as median norm.

  • Reformated heatmap. Includes adaptive text size based on number of rows, fixed color display for respecified and known positives genes, and an adaptive color wheel for multiple treatment groups.

MiRAnorm v0.2.0 (Release date 2016-04-07)

Changes:

  • Fixed number of cores for parallel to n.core = detectCores() - 1

  • Added parallel processing cluster.kappa function for Windows including automated detection.

  • Fixed a bug with norm.cluster when more than 1 group met the size criteria that caused function to throw an error due to dat structure.

  • Some variable name changes in miranorm

  • Updated deprecated commands from ggplot

  • Changed function name from normal.end to normal.selected to better reflect functionality

  • Added initial error checking for data structure to allow for only a single value for each Sample Gene combination.

  • Error checking for required names of dataset.

  • Warning implemented when less than 50% of the data meets user set criteria.

  • Volcano plot disabled until later versions and treatment group is clarified.

MiRAnorm v0.1.1 (Release date 2016-04-06)

Changes:

  • Minor visual fixes to ggplot figure to improve appearance

  • Fixed method="simple" conflict with still trying to create Clustplot in miranorm function.

MiRAnorm v0.1 (Release date 2016-04-05)

Changes:

  • First package build

Reference manual

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install.packages("MiRAnorm")

1.0.0 by Yuda Zhu, a year ago


Browse source code at https://github.com/cran/MiRAnorm


Authors: Yuda Zhu [aut, cre], Amanda Zhao [aut]


Documentation:   PDF Manual  


GPL-3 license


Imports grDevices, graphics, stats, utils, ggplot2, cluster, npmv, dendextend, parallel, MASS, plyr, reshape2, ArgumentCheck


See at CRAN