DEG_Pathway: A group of functions for Differential gene expression and...

In brightchan/cjbmisc:

Description

• get_sam4grp: generate tibble of library IDs according to the groups to be compared for DEG analysis

• get_compdf: wrapper using get_sam4grp to generate all pairwise or one-vs-all comparisons

• get_deg_EdgeR: generate DEG output with EdgeR

• get_deg_Deseq2: generate DEG output with DESeq2

• fgseaWrap: wrapper to run fgsea

• DEG_fgsea_Wrap: wrapper to run DESeq2 and fgsea

Usage

get_sam4grp(metadf, feat.coln, group1, group2, sample.coln, sep.grp = "+")

get_compdf(metadf, feat.coln, sample.coln, comp = "1vA", sep.grp = "+")

fgseaWrap(
  fn.gmt,
  ID.gene,
  stat.gene,
  nperm = 1000,
  minSize = 20,
  maxSize = 500,
  n.top = 10,
  fn.outp = NULL,
  dir.outp = NULL,
  outp.return = F
)

get_deg_EdgeR(
  countMat,
  name.feature,
  name.group1,
  name.group2,
  samID.grp1,
  samID.grp2,
  f.design = NULL,
  metadf = NULL,
  samID.coln = NULL,
  deseq.coln.trans = T,
  df.gene.anno = NULL,
  dir.outp = NULL,
  fn.outp = NULL
)

get_deg_Deseq2(
  countMat,
  name.feature,
  name.group1,
  name.group2,
  samID.grp1,
  samID.grp2,
  f.design = NULL,
  metadf = NULL,
  samID.coln = NULL,
  outpdir = NULL
)

DEG_fgsea_Wrap(
  countMat,
  name.feature,
  name.group1,
  name.group2,
  samID.grp1,
  samID.grp2,
  fn.gmt,
  f.design = NULL,
  metadf = NULL,
  samID.coln = NULL,
  outpdir = NULL
)

brightchan/cjbmisc documentation built on Nov. 5, 2021, 4:12 p.m.