Change Log

09/14/2015

A: Data:

1. Adding the CisBP data file for dm3(Drosophila_melanogaster)

2. Adding partial hg19.2bit, partial gencode GTF for chrmosome 19

3. Adding BED files from ChipSeq data for chrmosome 19

4. Adding PRO-seq data for chrmosome 19

5. some fake motif PWM files.

B: Source:

1. Adding function: CisBP.getTFinformation()

2. Adding slots "zip.date" for CisBP.db class

3. Adding slots "cluster" and "tf_missing", renaming slots "tf_info", removing TF_ID for tfbs class

4. Adding function: tfbs.importMotifs()

5. Adding function:tfbs.selectExpressedMotifs(), gene expression and motif filtering, separated from the constructor CisBP.createFromCisBP()

6. Renaming function: tfbs.enrichmentTest()

7. Adding new cluster (apcluster) for tfbs.clusterMotifs()

8. Renaming expected field for the results returned by tfbs.enrichmentTest()

9. Adding parameter gc.robust.rep, use.cluster, threshold.type for tfbs.enrichmentTest()

10. Adding parameter threshold.type for tfbs.scanTFsite()

11. Adding parameter enrichment.type and pv.threshold for tfbs.reportEnrichment()

12. The parameter orders are changed in some functions

10/6/2015

1. Changing lambda of Poisson distribution in gene expression for RNA-seq data

2. Changing q value in APcluster to 0.99

3. Fixing bugs in the function print.tfbs.finding() and summary.tfbs.finding()

4. Adding peak starting and ending positions for the results of matches option in the function tfbs.scanTFsite().

10/27/2015

1. Changing the return value of tfbs.selectByRandom() and tfbs.selectByGeneExp() and adding the indices of selected motif into the matrix tfbs@cluster.

12/2/2015

1. Implementing a parser to load motif data from the source other than Cis-BP, such as Transfac, jaspar, Meme and Mscan.

2. Drawing apcluster heatmap with same style as agnes results.

12/9/2015

1. Fixing a bug in tfbs.scanTFsite function with the option "maxposterior"

2. Tuning the package to pass the R package check(R CMD check rtfbsdb --as-cran), including NAMESPACE, DSCRIPTION and R codes.

3/28/2016 version 0.3.8

1. Adding the parameter "lowest.reads.RPKM" for tfbs.selectExpressedMotifs function

2. Adding the parameter "gc.correction.pvalue=0.01" for tfbs.enrichmentTest function

3. Adding the parameter "nrow.per.page" for tfbs.drawLogosForClusters function

4. Checking the unix commands or genomic tools if the system callings are failed.

5. Adding reads and lambda in RPKM unit in the expresslevel result.

6. Importing motifs from HOCOMOCO and MotifDB database.

4/6/2016 version 0.3.9

1. Samtools dependency is removed.

2. New function 'tfbs.plotEnrichment' is added to plot QQ-like plot for the p-values of enrichment result.