writeFilesTosent: Writes File used for follow up analyses in a folder

Description Usage Arguments Value

Description

Save the preprocessed data in a folder for further using filenames specified as parameters. Parameter 'file_renaming_samples_tosend' can specify a filename where a column named 'oldname' and 'newname' is provided in order to rename sample. Column oldname must match the names of the samples in column new_ID in the '$chipsamples' data.frame included in the HT12 object. Can be empty if no renaming is required

Usage

1
2
3
4
5
6
7
8
9
writeFilesTosend(ht12object, paramfile = NULL,
  file_sampleannot_final.txt = "from_paramfile",
  file_probeannot_final.txt = "from_paramfile",
  file_annot_final.xlsx = "from_paramfile",
  file_final_expression_set = "from_paramfile",
  file_final_expression_matrix = "from_paramfile",
  file_all_transcripts_good_incl_remapping_ok = "from_paramfile",
  file_final_expression_matrix_allProbes.txt = "from_paramfile",
  file_renaming_samples_tosend = "from_paramfile")

Arguments

ht12object

A list object of class HT12prepro created with function checkExtractChipsamples

paramfile

Path to the file specifying parameters

file_sampleannot_final.txt

default is sampleannot_HT12v4.txt Filename for sample-related attributes after finished preprocessing

file_probeannot_final.txt

Filename for expression probe-related attributes after finished preprocessing

file_annot_final.xlsx

Filename for an excel file combining 'file_sampleannot_final.txt' and 'file_probeannot_final.txt'.

file_final_expression_set

Filename of expression set after finished preprocessing

file_final_expression_matrix

Filename of expression matrix as R object after finished preprocessing

file_all_transcripts_good_incl_remapping_ok

Filename where probes are listed that are classified as expressed, not over-inflated for batch effects and classified at least 'good' according to remapping on the human genome as described in Nucleic Acids Res. Januar 2010;38(3):e17. in all user-provided subgroups

file_final_expression_matrix_allProbes.txt

Filename of expression matrix as tab delimited text file after finished preprocessing

file_renaming_samples_tosend

Filename where a column named 'oldname' and 'newname' is provided in order to rename samples, column oldname must match the names of the sample in column new_ID in the 'chipsamples' data.frame. Can be empty if no renaming is required

datafolder_results

directory of the resulting preprocessed data

Value

Written files defined in the parameters


holgerman/HT12ProcessoR documentation built on Sept. 6, 2018, 1:54 p.m.