mergeResults: Merge intermediate results of DEUS

In timjeske/DEUS: Differential expression of unique sequences

Description

The function merges results created during DEUS analysis into a comprehensive summary table. It is also possible to merge only a sub-set of all results or to generate the results with other methods than the provided ones.

Usage

mergeResults(de_result, count_stats, blast_result, clust_result, map)

Arguments

de_result	Result of differential expression analysis generated by runDESeq2 (columns 'Log2FoldChange', 'Pvalue' and 'IHWPvalue' are required)
count_stats	Means and standard deviations of each condition in analysis generated by getConditionCountStats
blast_result	Result of BLAST generated by runBlast (columns 'qseqid', 'sseqid', 'length' and 'evalue' are required)
clust_result	Result of clustering generated by runClustering
map	A data frame with sequences as row names and sequence identifiers in first column. Can be generated by createMap

Value

If all results are given, a data frame is created with sequences as row names and the columns 'SequenceID', 'Log2FoldChange', 'Pvalue', 'IHWPvalue', 'NormCounts_<cond1>_Mean', 'NormCounts_<cond1>_Sd', 'NormCounts_<cond2>_Mean', 'NormCounts_<cond2>_Sd', 'ClusterID', 'Length', 'BlastEvalue' and 'FeatureList'. If any result is not given corresponding columns are missing.

timjeske/DEUS documentation built on June 6, 2019, 12:59 p.m.