Up: Component summary Component

GenomeSlider

Summarized genomic events at sliding window intervals and/or at predifined regions. The summarizing function can be specified eg. mean, median, sum, max, min. Missing values are handled.

Version 1.0
Bundle sequencing
Categories Analysis
Authors Amjad Alkodsi (Amjad.Alkodsi@Helsinki.FI)
Issue tracker View/Report issues
Requires GenomicRanges (R-bioconductor)
Source files component.xml GenomeSlider.R
Usage Example with default values

Inputs

Name Type Mandatory Description
matrix CSV Mandatory Input csv file having the data to be summarized.
regions CSV Optional Predefined regions for which summarizing will be performed. If not provided, only sliding window will be performed.
chrLengths CSV Optional CSV file containing chromosome lengths. Needed only for sliding window summarization.

Outputs

Name Type Description
regionsSummary CSV Summarization over predifined regions.
windowsSummary CSV Summarization over sliding windows.

Parameters

Name Type Default Description
echoRegionColumns string "" Comma-separated column names for the columns from regions input to be echoed in the regionSummary output. If empty (default), no columns will be echoed.
func string "" The summarization function can be one of the following: "mean","median","sum","max","min". If empty string (default) was selected, the summarization will count events in matrix that overlaps with predefined regions or windows.
matrixCategoryColumn string "" Name of the column that has different categories. The output will have one column for each category in this column with values corresponding to category counts in each genomic region.
matrixCollapseColumn string "" Name of the column that has different categories or IDs. The output will have one column having collapsed (comma-separated) unique categories or IDs present in the coresponding genomic region.
matrixDataColumns string "" R expression for selecting the data columns in matrix input e.g. "c(1,2,3)", "1:3", "c('column1','column2','column3')". If empty (default), the summarization will count events in matrix that overlaps with predefined regions or windows.
matrixRegionColumns string "" Comma-separated column names for the chr-start-end columns in matrix input respectively. If empty (default), first three columns will be considered.
regionColumns string "" Comma-separated column names for the chr-start-end columns in regions input respectively. If empty (default), first three columns will be considered.
stepSize int 0 Step size for sliding window. If zero (default), non-overlapping windows will be generated.
windowSize int 1000 The size of sliding window.

Test cases

Test case Parameters IN
matrix
IN
regions
IN
chrLengths
OUT
regionsSummary
OUT
windowsSummary
case1 properties matrix regions chrLengths regionsSummary windowsSummary

windowSize=12,
matrixCollapseColumn=sample,
matrixCategoryColumn=type

case2 properties matrix regions chrLengths regionsSummary windowsSummary

windowSize=12,
stepSize=6,
matrixDataColumns=3:4,
matrixRegionColumns=chr,pos,pos,
regionColumns=chr,start,end,
echoRegionColumns=ID,
func=mean

case3 properties matrix regions chrLengths regionsSummary windowsSummary

windowSize=50,
stepSize=25,
matrixCollapseColumn=sample,
matrixCategoryColumn=transcriptionFactor


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