Man pages for drmjc/mjcaffy
Affymetrix helper functions

affy.pivot.tablemerge expression and calls together
batchRMARMA normalize in batches
boxplot_affy_probetypesAffymetrix boxplot of probe types
calls2colourConvert Affymetrix MAS5 calls into colours.
cdfName-methodsExtract the CDF file name from a CEL file header.
celDatedatestamp of Affymetrix CEL file
dabg2callsConvert DABG P-values into P/M/A calls
find.nuse.cutofffind a NUSE cutoff
fitPLM.STarraysfitPLM model on Affymetrix ST arrays
hist_affycallsPlot a histogram of affy P/M/A calls.
hist_array_rankshistogram of array ranks
hist_DABGPlot a histogram of DABG values
hist_Pcount_cumulativePlot a cumulative histogram of affy P/M/A calls.
import.APTImport a file produced by APT.
import.dabgImport DABG results
import.mpsImport an Affymetrix MPS file
import.netaffx.csvimport Affymetrix NetAffx csv file
make.GSEA.chip.affySTConvert Affymetrix ST array to CHIP file
mjcaffy-packageHelper functions for dealing with Affymetrix data.
mps2envConvert an Affymetrix MPS object into a hash table (an R...
mps2listConvert an an Affymetrix MPS table into a named list, mapping...
mps2mapConvert an Affymetrix MPS object into a 2column map, where...
parse.affy.aptparse Affymetrix gene info tables for ST arrays
parse.affy.gffparse.affy.gff
parse.affy.ST.array.annotationparse an Affymetrix Gene or Exon ST transcript.csv file
plot_rma_vs_callsplot a distribution of RMA data, split by the affy P/M/A...
readCELFunction to import an Affymetrix CEL file
run.dabgrun Affymetrix DABG algorithm
test_parse.affy.ST.array.annotationtest_parse.affy.ST.array.annotation
drmjc/mjcaffy documentation built on May 13, 2017, 6:43 a.m.