anamiR: anamiR: An integrated analysis package of miRNA and mRNA...

In AllenTiTaiWang/anamiR: An integrated analysis package of miRNA and mRNA expression data

Description

The anamiR package is used to identify miRNA-target genes interactions. The anamiR package provides a whole workflow, which contains important functions: 'normalization', 'differExp_discrete', 'negative_cor', 'miR_converter', 'database_support', 'enrichment'.

normalization

The normalization function is used to normalize the expression data with one of three methods, including normal, quantile, rank.invariant.

differExp_discrete

The differExp_discrete function is used to find the differential genes or miRNAs from given expression data with one of three statistical methods, including t.test, wilcox.test,limma and DESeq. The miRNA would remain if its p-value lower than the cutoff value.

miR_converter

The miR_annotation function is used to convert the older miRNA annotation to the miRBase 21 version.

negative_cor

The negative_cor function is used to identify the possible miRNA-target gene interactions from given miRNA and mRNA expression data by caculating the correlation coefficient between each miRNA and gene. interaction would remain if its correlation coefficient is negative and lower than cutoff value.

database_support

The database_support function would search information about miRNA-target gene interactions from an integrated database, which contains 8 algorithm predicted databases and 2 experiment validated databases. Eventually return a big table, which is in data.frame format and contains extra 10 columns for those 10 databases to count if interactions were predicted or validated by these databases.

enrichment

The enrichment function is used to do the functional analysis from the output of 'database_support'. Not only p-value from hypergeometric test but empirical p-value from 10000 times of permutation would be provided by this function.

AllenTiTaiWang/anamiR documentation built on May 5, 2019, 4:55 a.m.