DESeqDataSetFromSlidingWindows {DEWSeq} | R Documentation

## create DESeq data object

### Description

create DESeq data object from sliding window counts, phenotype data and annotation data

### Usage

    DESeqDataSetFromSlidingWindows(countData, colData, annotObj, design,
      tidy = FALSE, ignoreRank = FALSE, start0based = TRUE)

### Arguments

`countData` | `data.frame` or `matrix`, sliding window count data
`colData` | `DataFrame` or `data.frame`, phenotype data, see `DESeqDataSet`
`annotObj` | `data.frame` or `character`, can either be a data.frame or a file name, see details
`design` | `formula` or `matrix`, design of the experiment, see `DESeqDataSet`
`tidy` | `logical`, If TRUE, first column is of countData is treated as rownames (defalt: FALSE), see `DESeqDataSet`
`ignoreRank` | `logical`, ignore rank, see `DESeqDataSet`
`start0based` | `logical`, TRUE (default) or FALSE. If TRUE, then the start positions in `annotObj` is considered to be 0-based

### Details

If `annotObj` is a file name, the input file MUST be <TAB> separated, and supports reading in .gz files.
If `annotObj` is a data.frame, `colnames(annotObj)` MUST not be empty.
This function checks for the following columns after reading in the file or on data.frame:

- `chromosome`: chromosome name

- `unique_id`: unique id of the window, `rownames(object)` must match this column

- `begin`: window start co-ordinate, see parameter `start0based`

- `end`: window end co-ordinate

- `strand`: strand

- `gene_id`: gene id

- `gene_name`: gene name

- `gene_type`: gene type annotation

- `gene_region`: gene region

- `Nr_of_region`: number of the current region

- `Total_nr_of_region`: total number of regions

- `window_number`: window number

This function creates a `DESeqDataSet` using supplied countData, phenotype data and annotation data. The chromosomal locations and annotations of the sliding windows (parsed from `annotObj`) can be accessed from the returned object using: `rowRanges(object)`

### Value

DESeq object

### Examples

    data("SLBP_K562_w50s20")
    slbpDat <- counts(SLBP_K562_w50s20)
    phenoDat <- DataFrame(conditions=as.factor(c(rep('IP',2),'SMI')),
    row.names = colnames(slbpDat))
    phenoDat$conditions <- relevel(phenoDat$conditions,ref='SMI')
    annotDat <- as.data.frame(rowRanges(SLBP_K562_w50s20))
    # by default chromsome column is 'seqnames'
    # and begin co-ordinate column is 'start'
    # rename these columns
    colnames(annotDat)[1:2] <- c('chromosome','begin')
    slbpDds <- DESeqDataSetFromSlidingWindows(countData = slbpDat,
    colData = phenoDat,annotObj = annotDat,design=~conditions)

[Package DEWSeq version 1.6.0 Index]