get_sample_information: Create sample information dataframe
In lakhanp1/chipmine: Analyze ChIP-seq Data

Description Usage Arguments Value Examples

View source: R/p01_get_sample_information.R

This is a utility function to prepare the sample information dataframe for sample of interest using experiment information file. Experiment information file should have columns: sampleId, IP_tag, control, peakType.

Possible values for compulsory columns and how they are handled:

IP_tag: One of c("HA", "FLAG", "HIS", "MYC", "TAP", "TF", "polII"). This column value is used to determine whether the ChIPseq data is for polII ChIPseq or transcription factor ChIPseq. If polII ChIPseq, polIIExpFile, polIIExpMat columns are populated with appropriate file names for polII data.
peakType: One of c("narrowPeak", "broadPeak"). This column value is used to decide the macs2 peak output file name (i.e. narrowPeak or broadPeak).
control: This column value is used to decide the suffix of macs2 output files. If the value is blank or ".", withoutCtrl is used in macs2 peak realated file names and withCtrl otherwise.

get_sample_information(
  exptInfoFile,
  samples = NULL,
  dataPath,
  profileMatrixSuffix = "normalizedmatrix",
  profileType = "profile"
)

`exptInfoFile`	A tabular file with details for each sample. "sampleId" and "IP_tag" columns are must
`samples`	A vector of Sample IDs which are to be processed. Default: All samples are used
`dataPath`	Path where the data is stored
`profileMatrixSuffix`	A character string to be used in the file name of profile matrix file. Generating profile matrix takes long time and hence it is efficient to save the profile matrix. If profile matrix is saved, this suffix is used to design the name of profile matrix file. This will generate a file name "sample_ID.normalizedMatrix.tab.gz". Different intutuve suffixes can be used to store profile matrix like TSS_4kb_2kb_normalized, TSS_3kb_3kb_normalized, normalizedmatrix_5kb, etc. Default: normalizedmatrix.
`profileType`	Type of profile. This will be added as suffix to the profile name

Data frame with columns "sampleId", "IP_tag", "control", "peakType", "sampleName", "profileName", "bwFile", "matFile", "clusterFile", "mergedDataFile", "polIIExpFile", "polIIExpMat", "peakFile", "peakAnno", "peakTargetFile", "FE_bwFile".