Pipe FASTQ files to SeuratObject and DESeqDataSet.

Usage

Fastq2R(
  sample.dir,
  ref,
  method = c("CellRanger", "STAR"),
  localcores = 4,
  localmem = 16,
  out.folder = NULL,
  st.path = NULL,
  st.paras = "--chemistry=auto --jobmode=local",
  merge = TRUE,
  count.col = 2,
  meta.data = NULL,
  fmu = NULL
)

Arguments

sample.dir: Vector of path to samples (contain fastq files), e.g. c("path/to/GSM1111", "path/to/GSM2222","path/to/GSM3333").
ref: Path of folder containing 10x-compatible transcriptome RunCellRanger STAR RunSTAR reference.
method: Mapping methods, choose from CellRanger (10x Genomics) and STAR (Smart-seq2 or bulk RNA-seq). Default: CellRanger.
localcores: The max cores/thread used RunCellRanger/RunSTAR. Default: 4.
localmem: The max memory (GB) used RunCellRanger. Default: 16.
out.folder: Output folder. Default: NULL (current working directory).
st.path: Path to STAR or cellranger. Default: NULL (conduct automatic detection).
st.paras: Parameters for STAR or cellranger. Default: "–chemistry=auto –jobmode=local".
merge: Logical, whether to merge the SeuratObjects, use when method is CellRanger. Default: TRUE.
count.col: Column contains used count data (2: unstranded; 3: stranded=yes; 4: stranded=reverse), use when method is STAR. Default: 2.
meta.data: Dataframe contains sample information for DESeqDataSet, use when method is STAR. Default: NULL.
fmu: Column of meta.data contains group information. Default: NULL.

Value

SeuratObject, DESeqDataSet or NULL.

Examples

if (FALSE) { # \dontrun{
# run CellRanger (10x Genomics)
# the sample.dir (can be a vector) corresponding to sra.folder/GSMXXXX (SplitSRA) or out.folder/GSMXXXX (DownloadFastq)
seu <- Fastq2R(
  sample.dir = "/path/to/fastq",
  ref = "/path/to/10x/ref",
  method = "CellRanger",
  out.folder = "/path/to/results",
  st.path = "/path/to/cellranger"
)
# run STAR (Smart-seq2 or bulk RNA-seq)
# the sample.dir (can be a vector) corresponding to sra.folder/GSMXXXX (SplitSRA) or out.folder/GSMXXXX (DownloadFastq)
deobj <- Fastq2R(
  sample.dir = "/path/to/fastq",
  ref = "/path/to/star/ref",
  method = "STAR",
  out.folder = "/path/to/results",
  st.path = "/path/to/STAR",
  st.paras = "--outBAMsortingThreadN 4 --twopassMode None"
)
} # }