DESeqDataSetFromSlidingWindows: create DESeq data object

In EMBL-Hentze-group/DEWSeq: Differential Expressed Windows Based on Negative Binomial Distribution

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)

EMBL-Hentze-group/DEWSeq documentation built on Oct. 17, 2023, 10:41 p.m.