For sleuth_gene_table, sleuth_results, and sleuth_to_matrix

Updated sleuth_gene_table, sleuth_prep, sleuth_wt, sleuth_fit, and
models.

More precise definition of num_transcripts

…terlab#64)

temporarily disable filtering at gene level #vc

stash gene mode #vc

work in progress #vc

add functionality to filter by target id #vc

update aggregation #vc

comment out a section in aggregation #vc

deal with intersection #vc

first cut at empirical bayes #vc

fix small bug in empirical bayes #vc

testing out pmax #vc

empirical bayes and propagate filter #vc

norm by effective length

massive cleanup

more cleaning

refactor out check target mapping

remove filter by target_id

update warnings in check_target_mapping

more cleanup

Gene aggregation

update vignette

…dded sleuth_prep option to select number of cores for mclapply

…ons for num_cores to throw informative error

…trix did not have dim names that matched the formula or the sample ids

… of s2c

… option into 'spread_abundance_by' to prevent downstream error when preparing just one sample

…achterlab#86

…trary string can be used as a sample name; proposed solution for pachterlab#89

+ move over gene_summary code
+ sleuth object now reports gene-level info for obs_norm and obs_norm_filt

…p for loop of sleuth_prep

…avoid a bug related to using the bs_mat in bs_quant_tpm

…m and bs_mat gene aggregation

…-level analysis

+matrixStats (using which_agg_id vs which_transcript_id)
+colnames of bs_mat
+names of sigma_q_sq

+ change gene-level conditionals to ret$gene_mode

…vel code

…later commits

…ocumentation

…savings features

…formation function used

…he transform function after fits have already been made

+ any change to transform_fxn leads to all existing fits have 'FALSE' transform_synced statuses
+ the user is warned that all existing fits need to be redone.

+ switch order of @example and @export to prevent error (newbie mistake)
+ comment out reference to 'num_cores' for time being (not currently used)

+ User is now warned to re-do both sleuth_prep and sleuth_fit, since changing transform_fxn also affects bootstrap summaries
+ Bug 1: transform function was applied twice; now only applied in sleuth_prep
+ Bug 2: checks for transform sync status in sleuth_lrt referred to wrong variable

…iable for obs_norm_gene and tpm_norm_gene

…e syntax rather than dplyr

… pared down target_mapping table

…es leads to downstream errors when doing gene aggregation

…lumn

+ make sure blank entries are treated as NA values
+ fix behavior of overall list of gene IDs for gene-level filter_bool

+ this processed data uses the full target mappings
+ also includes TPM calculations for the bootstraps and the extra_bootstrap_summary
+ update Ellahi dataset README with info on the preprocessed results

…eparation for parallelization